Literature DB >> 22347124

Methyl 3-O-α-l-fucopyranosyl α-d-gal-acto-pyran-oside: a synchrotron study.

Lars Eriksson, Göran Widmalm.   

Abstract

The title compound, C(13)H(24)O(10) is the methyl glycoside of a structural element α-l-Fucp-(1→ 3)-α-d-Galp making up two thirds of the repeating unit in the capsular polysaccharide of Klebsiella K63. The conformation of the title compound is described by the glycosidic torsion angles ϕ(H) = 55 (1)° and ψ(H) = -24 (1)°. The hy-droxy-methyl group in the galactose residue is present in the gauche-trans conformation. In the crystal, O-H⋯O hydrogen bonds connect the disaccharide units into chains along the a-axis direction and further hydrogen bonds cross-link the chains.

Entities:  

Year:  2012        PMID： 22347124      PMCID： PMC3275268          DOI： 10.1107/S1600536812002279

Source DB:  PubMed          Journal:  Acta Crystallogr Sect E Struct Rep Online        ISSN： 1600-5368


Related literature

The capsular polysaccharide (CPS) of Klebsiella K63 contains a repeating unit consisting of → 3)-α-d-GalpA–(1 → 3)-α-l-Fucp-(1 → 3)-α-d-Galp-(1 →, see: Joseleau & Marais (1979 ▶). For an investigation of the CPS S-156 from Klebsiella pneumoniae ATCC 316 46, see: Johansson et al. (1994 ▶) and of the CPS from Klebsiella pneumoniae I-1507, see: Guetta et al. (2003 ▶). For a fiber X-ray diffraction study of the Klebsiella K63 CPS, see: Elloway et al. (1980 ▶). For the synthesis, see: Baumann et al. (1988 ▶).

Experimental

Crystal data

C13H24O10 M = 340.32 Orthorhombic, a = 4.78478 (11) Å b = 15.7859 (5) Å c = 19.4401 (5) Å V = 1468.36 (7) Å3 Z = 4 Synchrotron radiation λ = 0.907 Å μ = 0.13 mm−1 T = 100 K 0.03 × 0.01 × 0.01 mm

Data collection

Marresearch MARCCD 165 diffractometer 7469 measured reflections 1162 independent reflections 975 reflections with I > 2σ(I) R int = 0.117 θmax = 30.1°

Refinement

R[F 2 > 2σ(F 2)] = 0.060 wR(F 2) = 0.177 S = 1.09 1162 reflections 216 parameters H-atom parameters constrained Δρmax = 0.30 e Å−3 Δρmin = −0.27 e Å−3 Data collection: MARCCD (Marresearch, 2010 ▶); cell refinement: CrysAlis RED (Oxford Diffraction, 2008 ▶); data reduction: CrysAlis RED; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: DIAMOND (Brandenburg, 1999 ▶); software used to prepare material for publication: PLATON (Spek, 2009 ▶). Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S1600536812002279/hb6569sup1.cif Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536812002279/hb6569Isup2.hkl Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C13H24O10Z = 4
Mr = 340.32F(000) = 728
Orthorhombic, P212121Dx = 1.539 Mg m−3
Hall symbol: P 2ac 2abSynchrotron radiation, λ = 0.907 Å
a = 4.78478 (11) ŵ = 0.13 mm−1
b = 15.7859 (5) ÅT = 100 K
c = 19.4401 (5) ÅPrism, colorless
V = 1468.36 (7) Å30.03 × 0.01 × 0.01 mm
Marresearch MARCCD 165 diffractometer975 reflections with I > 2σ(I)
Radiation source: I911, MaxlabRint = 0.117
Si(111)θmax = 30.1°, θmin = 3.1°
Detector resolution: 0.0806 pixels mm-1h = −5→5
φ scansk = −17→17
7469 measured reflectionsl = −20→20
1162 independent reflections
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.060Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.177H-atom parameters constrained
S = 1.09w = 1/[σ2(Fo2) + (0.1211P)2 + 0.7072P] where P = (Fo2 + 2Fc2)/3
1162 reflections(Δ/σ)max < 0.001
216 parametersΔρmax = 0.30 e Å−3
0 restraintsΔρmin = −0.27 e Å−3
Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes.
Refinement. Refinement of F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > σ(F2) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.
xyzUiso*/Ueq
C1F0.2242 (15)0.5346 (4)0.5260 (3)0.0359 (16)
H1F0.09170.58020.51140.054*
C2F0.3048 (14)0.4827 (5)0.4636 (3)0.0409 (17)
H2F0.12700.46330.44160.061*
C3F0.4713 (14)0.4025 (4)0.4827 (3)0.0394 (17)
H3F0.65770.42170.49990.059*
C4F0.3298 (15)0.3548 (5)0.5419 (3)0.0382 (17)
H4F0.45710.30890.55850.057*
C5F0.2588 (15)0.4126 (4)0.6012 (3)0.0403 (17)
H5F0.43680.43470.62140.060*
O5F0.0941 (9)0.4845 (3)0.5765 (2)0.0393 (12)
C6F0.0937 (17)0.3710 (5)0.6571 (3)0.0465 (19)
H6F10.05330.41240.69330.070*
H6F20.20170.32400.67640.070*
H6F3−0.08220.34940.63810.070*
O2F0.4489 (10)0.5325 (3)0.4138 (2)0.0430 (13)
H2F10.56240.56480.43380.065*
O3F0.5214 (11)0.3485 (3)0.4262 (2)0.0458 (13)
H3F10.37250.34170.40400.069*
O4F0.0806 (9)0.3171 (3)0.5133 (3)0.0430 (13)
H4F10.05320.26970.53160.065*
C1G0.6262 (16)0.7690 (5)0.6550 (3)0.0400 (17)
H1G0.77960.81130.64870.060*
C2G0.6339 (14)0.7069 (4)0.5935 (3)0.0371 (17)
H2G0.82640.68230.59090.056*
C3G0.4279 (14)0.6336 (4)0.6047 (3)0.0362 (16)
H3G0.23210.65540.60170.054*
C4G0.4759 (15)0.5952 (5)0.6746 (4)0.0406 (18)
H4G0.32890.55140.68310.061*
C5G0.4618 (15)0.6608 (4)0.7312 (4)0.0420 (18)
H5G0.27010.68600.73280.063*
C6G0.5295 (18)0.6222 (5)0.7996 (3)0.0463 (19)
H6G10.41760.57000.80590.069*
H6G20.72950.60620.80060.069*
O1G0.3648 (10)0.8128 (3)0.6509 (2)0.0434 (13)
O2G0.5808 (10)0.7497 (3)0.5311 (2)0.0436 (13)
H2G10.70440.73700.50220.065*
O3G0.4759 (10)0.5731 (3)0.5507 (2)0.0412 (12)
O4G0.7492 (10)0.5552 (3)0.6797 (2)0.0444 (13)
H4G10.79040.53290.64180.067*
O5G0.6680 (10)0.7279 (3)0.7175 (2)0.0418 (13)
O6G0.4725 (10)0.6796 (3)0.8553 (2)0.0446 (13)
H6G0.59700.67480.88550.067*
C70.3647 (18)0.8825 (5)0.6975 (3)0.049 (2)
H7A0.38420.86150.74470.073*
H7B0.18850.91370.69310.073*
H7C0.52130.92020.68670.073*
U11U22U33U12U13U23
C1F0.026 (3)0.053 (4)0.029 (3)0.002 (3)−0.004 (3)−0.006 (3)
C2F0.021 (3)0.061 (4)0.041 (4)−0.004 (3)−0.012 (3)0.005 (4)
C3F0.025 (3)0.058 (4)0.035 (4)−0.001 (4)−0.003 (3)−0.007 (3)
C4F0.028 (4)0.051 (4)0.035 (4)−0.004 (3)−0.007 (3)−0.005 (3)
C5F0.024 (3)0.054 (4)0.044 (4)0.005 (4)−0.003 (3)0.006 (3)
O5F0.023 (2)0.057 (3)0.038 (3)0.000 (2)0.002 (2)0.002 (2)
C6F0.038 (4)0.062 (5)0.040 (4)0.007 (4)0.001 (3)0.000 (4)
O2F0.030 (3)0.061 (3)0.038 (2)−0.004 (2)0.004 (2)0.000 (2)
O3F0.026 (3)0.067 (3)0.044 (3)0.000 (3)−0.002 (2)−0.001 (2)
O4F0.023 (3)0.058 (3)0.048 (3)−0.005 (2)0.000 (2)−0.001 (2)
C1G0.036 (4)0.051 (4)0.032 (4)0.005 (4)0.001 (3)0.007 (3)
C2G0.020 (3)0.059 (4)0.032 (3)0.006 (3)0.001 (3)0.000 (3)
C3G0.020 (3)0.049 (4)0.040 (4)0.001 (3)−0.012 (3)−0.003 (3)
C4G0.021 (3)0.051 (4)0.050 (4)0.005 (3)−0.007 (3)0.000 (4)
C5G0.025 (4)0.059 (5)0.043 (4)0.002 (4)−0.002 (3)0.002 (3)
C6G0.047 (5)0.055 (4)0.037 (4)0.006 (4)−0.002 (4)−0.004 (4)
O1G0.029 (3)0.059 (3)0.042 (3)0.006 (3)−0.006 (2)0.006 (2)
O2G0.023 (3)0.071 (3)0.038 (2)0.008 (3)0.002 (2)0.008 (3)
O3G0.025 (3)0.058 (3)0.041 (3)0.000 (2)−0.009 (2)−0.002 (2)
O4G0.031 (3)0.063 (3)0.040 (3)0.010 (3)0.003 (2)−0.006 (2)
O5G0.028 (3)0.061 (3)0.037 (3)−0.005 (2)−0.002 (2)0.000 (2)
O6G0.029 (3)0.069 (3)0.036 (3)−0.003 (3)−0.002 (2)−0.004 (3)
C70.042 (4)0.068 (5)0.036 (4)0.010 (4)−0.008 (3)−0.004 (4)
C1F—O5F1.406 (8)C1G—C2G1.546 (9)
C1F—O3G1.432 (8)C1G—H1G1.0000
C1F—C2F1.515 (9)C2G—O2G1.414 (8)
C1F—H1F1.0000C2G—C3G1.535 (9)
C2F—O2F1.425 (8)C2G—H2G1.0000
C2F—C3F1.541 (10)C3G—O3G1.438 (8)
C2F—H2F1.0000C3G—C4G1.505 (9)
C3F—O3F1.411 (8)C3G—H3G1.0000
C3F—C4F1.532 (10)C4G—O4G1.456 (9)
C3F—H3F1.0000C4G—C5G1.513 (10)
C4F—O4F1.444 (8)C4G—H4G1.0000
C4F—C5F1.509 (9)C5G—O5G1.471 (8)
C4F—H4F1.0000C5G—C6G1.498 (10)
C5F—O5F1.462 (8)C5G—H5G1.0000
C5F—C6F1.495 (10)C6G—O6G1.437 (8)
C5F—H5F1.0000C6G—H6G10.9900
C6F—H6F10.9800C6G—H6G20.9900
C6F—H6F20.9800O1G—C71.424 (8)
C6F—H6F30.9800O2G—H2G10.8400
O2F—H2F10.8400O4G—H4G10.8400
O3F—H3F10.8400O6G—H6G0.8400
O4F—H4F10.8400C7—H7A0.9800
C1G—O5G1.392 (8)C7—H7B0.9800
C1G—O1G1.431 (9)C7—H7C0.9800
O5F—C1F—O3G112.2 (5)O1G—C1G—H1G108.2
O5F—C1F—C2F111.6 (5)C2G—C1G—H1G108.2
O3G—C1F—C2F106.5 (5)O2G—C2G—C3G111.5 (5)
O5F—C1F—H1F108.8O2G—C2G—C1G110.9 (5)
O3G—C1F—H1F108.8C3G—C2G—C1G110.7 (5)
C2F—C1F—H1F108.8O2G—C2G—H2G107.9
O2F—C2F—C1F111.7 (6)C3G—C2G—H2G107.9
O2F—C2F—C3F111.5 (5)C1G—C2G—H2G107.9
C1F—C2F—C3F112.5 (5)O3G—C3G—C4G111.5 (5)
O2F—C2F—H2F106.9O3G—C3G—C2G107.1 (5)
C1F—C2F—H2F106.9C4G—C3G—C2G109.5 (5)
C3F—C2F—H2F106.9O3G—C3G—H3G109.6
O3F—C3F—C4F111.3 (6)C4G—C3G—H3G109.6
O3F—C3F—C2F113.4 (5)C2G—C3G—H3G109.6
C4F—C3F—C2F110.9 (6)O4G—C4G—C3G111.9 (6)
O3F—C3F—H3F107.0O4G—C4G—C5G106.7 (6)
C4F—C3F—H3F107.0C3G—C4G—C5G112.0 (6)
C2F—C3F—H3F107.0O4G—C4G—H4G108.7
O4F—C4F—C5F110.9 (6)C3G—C4G—H4G108.7
O4F—C4F—C3F106.1 (5)C5G—C4G—H4G108.7
C5F—C4F—C3F112.1 (6)O5G—C5G—C6G108.0 (6)
O4F—C4F—H4F109.2O5G—C5G—C4G109.2 (6)
C5F—C4F—H4F109.2C6G—C5G—C4G111.0 (6)
C3F—C4F—H4F109.2O5G—C5G—H5G109.5
O5F—C5F—C6F107.1 (6)C6G—C5G—H5G109.5
O5F—C5F—C4F109.8 (5)C4G—C5G—H5G109.5
C6F—C5F—C4F114.1 (6)O6G—C6G—C5G111.7 (6)
O5F—C5F—H5F108.5O6G—C6G—H6G1109.3
C6F—C5F—H5F108.5C5G—C6G—H6G1109.3
C4F—C5F—H5F108.5O6G—C6G—H6G2109.3
C1F—O5F—C5F115.3 (5)C5G—C6G—H6G2109.3
C5F—C6F—H6F1109.5H6G1—C6G—H6G2107.9
C5F—C6F—H6F2109.5C7—O1G—C1G109.8 (5)
H6F1—C6F—H6F2109.5C2G—O2G—H2G1109.5
C5F—C6F—H6F3109.5C1F—O3G—C3G113.1 (5)
H6F1—C6F—H6F3109.5C4G—O4G—H4G1109.5
H6F2—C6F—H6F3109.5C1G—O5G—C5G113.4 (5)
C2F—O2F—H2F1109.5C6G—O6G—H6G109.5
C3F—O3F—H3F1109.5O1G—C7—H7A109.5
C4F—O4F—H4F1109.5O1G—C7—H7B109.5
O5G—C1G—O1G113.5 (5)H7A—C7—H7B109.5
O5G—C1G—C2G112.0 (5)O1G—C7—H7C109.5
O1G—C1G—C2G106.6 (5)H7A—C7—H7C109.5
O5G—C1G—H1G108.2H7B—C7—H7C109.5
O5F—C1F—C2F—O2F−177.1 (5)O2G—C2G—C3G—O3G64.1 (6)
O3G—C1F—C2F—O2F−54.4 (7)C1G—C2G—C3G—O3G−172.1 (5)
O5F—C1F—C2F—C3F−50.8 (7)O2G—C2G—C3G—C4G−174.9 (5)
O3G—C1F—C2F—C3F71.9 (7)C1G—C2G—C3G—C4G−51.0 (7)
O2F—C2F—C3F—O3F−60.3 (8)O3G—C3G—C4G—O4G53.0 (7)
C1F—C2F—C3F—O3F173.3 (6)C2G—C3G—C4G—O4G−65.3 (7)
O2F—C2F—C3F—C4F173.7 (5)O3G—C3G—C4G—C5G172.8 (6)
C1F—C2F—C3F—C4F47.3 (7)C2G—C3G—C4G—C5G54.4 (7)
O3F—C3F—C4F—O4F−55.3 (7)O4G—C4G—C5G—O5G65.6 (6)
C2F—C3F—C4F—O4F71.8 (6)C3G—C4G—C5G—O5G−57.1 (7)
O3F—C3F—C4F—C5F−176.6 (6)O4G—C4G—C5G—C6G−53.3 (8)
C2F—C3F—C4F—C5F−49.5 (7)C3G—C4G—C5G—C6G−176.1 (6)
O4F—C4F—C5F—O5F−64.9 (7)O5G—C5G—C6G—O6G69.9 (7)
C3F—C4F—C5F—O5F53.6 (7)C4G—C5G—C6G—O6G−170.4 (6)
O4F—C4F—C5F—C6F55.4 (8)O5G—C1G—O1G—C767.5 (7)
C3F—C4F—C5F—C6F173.9 (6)C2G—C1G—O1G—C7−168.6 (5)
O3G—C1F—O5F—C5F−61.8 (6)O5F—C1F—O3G—C3G−65.4 (7)
C2F—C1F—O5F—C5F57.6 (7)C2F—C1F—O3G—C3G172.3 (5)
C6F—C5F—O5F—C1F176.5 (5)C4G—C3G—O3G—C1F97.7 (6)
C4F—C5F—O5F—C1F−59.0 (7)C2G—C3G—O3G—C1F−142.5 (5)
O5G—C1G—C2G—O2G177.9 (5)O1G—C1G—O5G—C5G62.6 (7)
O1G—C1G—C2G—O2G53.1 (7)C2G—C1G—O5G—C5G−58.2 (7)
O5G—C1G—C2G—C3G53.6 (7)C6G—C5G—O5G—C1G−179.8 (5)
O1G—C1G—C2G—C3G−71.1 (6)C4G—C5G—O5G—C1G59.4 (7)
D—H···AD—HH···AD···AD—H···A
O3f—H3f1···O6gi0.841.932.772 (7)177
O4f—H4f1···O3fii0.842.042.880 (7)175
O2g—H2g1···O2giii0.841.922.680 (7)149
O4g—H4g1···O5fiv0.842.082.827 (6)149
O6g—H6g···O3fv0.842.022.822 (7)158
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯AD—HH⋯AD⋯AD—H⋯A
O3f—H3f1⋯O6gi0.841.932.772 (7)177
O4f—H4f1⋯O3fii0.842.042.880 (7)175
O2g—H2g1⋯O2giii0.841.922.680 (7)149
O4g—H4g1⋯O5fiv0.842.082.827 (6)149
O6g—H6g⋯O3fv0.842.022.822 (7)158

Symmetry codes: (i) ; (ii) ; (iii) ; (iv) ; (v) .

  5 in total

1.  A short history of SHELX.

Authors:  George M Sheldrick
Journal:  Acta Crystallogr A       Date:  2007-12-21       Impact factor: 2.290

2.  Structure of the polysaccharide S-156 elaborated by Klebsiella pneumoniae ATCC 316 46.

Authors:  A Johansson; P E Jansson; G Widmalm
Journal:  Carbohydr Res       Date:  1994-02-03       Impact factor: 2.104

3.  Structure and properties of a bacterial polysaccharide named Fucogel.

Authors:  O Guetta; K Mazeau; R Auzely; M Milas; M Rinaudo
Journal:  Biomacromolecules       Date:  2003 Sep-Oct       Impact factor: 6.988

4.  Structure of the capsular polysaccharide of Klebsiella K-type 63.

Authors:  J P Joseleau; M F Marais
Journal:  Carbohydr Res       Date:  1979-12       Impact factor: 2.104

5.  Structure validation in chemical crystallography.

Authors:  Anthony L Spek
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2009-01-20
  5 in total
  1 in total

1.  Methyl 3-O-α-l-fucopyranosyl β-d-glucopyran-oside tetra-hydrate.

Authors:  Lars Eriksson; Göran Widmalm
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2012-10-20
  1 in total

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