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- PDB-4uap: X-ray structure of GH31 CBM32-2 bound to GalNAc -

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Basic information

Entry
Database: PDB / ID: 4uap
TitleX-ray structure of GH31 CBM32-2 bound to GalNAc
ComponentsGlycosyl hydrolase, family 31/fibronectin type III domain protein
KeywordsSUGAR BINDING PROTEIN / carbohydrate-binding module / B-sandwich / GalNAc
Function / homology
Function and homology information


polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / metal ion binding
Similarity search - Function
Alpha-glucosidase, N-terminal / : / Domain of unknown function DUF5110 / Domain of unknown function (DUF5110) / Bacterial Ig-like domain (group 2) / Invasin/intimin cell-adhesion fragments / Glycoside hydrolase family 31, N-terminal domain / Glycosyl hydrolase 31 N-terminal galactose mutarotase-like domain / Bacterial Ig-like domain 2 / Bacterial Ig-like domain, group 2 ...Alpha-glucosidase, N-terminal / : / Domain of unknown function DUF5110 / Domain of unknown function (DUF5110) / Bacterial Ig-like domain (group 2) / Invasin/intimin cell-adhesion fragments / Glycoside hydrolase family 31, N-terminal domain / Glycosyl hydrolase 31 N-terminal galactose mutarotase-like domain / Bacterial Ig-like domain 2 / Bacterial Ig-like domain, group 2 / : / Glycosyl hydrolase family 31 C-terminal domain / Glycoside hydrolase family 31 / Glycosyl hydrolases family 31 TIM-barrel domain / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / CBM2/CBM3, carbohydrate-binding domain superfamily / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Galactose mutarotase-like domain superfamily / Galactose-binding domain-like / Glycosyl hydrolase, all-beta / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Galactose-binding-like domain superfamily / Fibronectin type III / Fibronectin type III superfamily / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / Glycoside hydrolase superfamily / Jelly Rolls / Immunoglobulin-like fold / Sandwich / Mainly Beta
Similarity search - Domain/homology
2-acetamido-2-deoxy-beta-D-galactopyranose / Glycosyl hydrolase, family 31/fibronectin type III domain protein / Glycosyl hydrolase, family 31/fibronectin type III domain protein
Similarity search - Component
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsGrondin, J.M. / Abe, K. / Boraston, A.B. / Smith, S.P.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP 68913 Canada
CitationJournal: PLoS ONE / Year: 2017
Title: Diverse modes of galacto-specific carbohydrate recognition by a family 31 glycoside hydrolase from Clostridium perfringens.
Authors: Grondin, J.M. / Duan, D. / Kirlin, A.C. / Abe, K.T. / Chitayat, S. / Spencer, H.L. / Spencer, C. / Campigotto, A. / Houliston, S. / Arrowsmith, C.H. / Allingham, J.S. / Boraston, A.B. / Smith, S.P.
History
DepositionAug 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2017Group: Database references
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycosyl hydrolase, family 31/fibronectin type III domain protein
B: Glycosyl hydrolase, family 31/fibronectin type III domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5368
Polymers33,8302
Non-polymers7076
Water6,341352
1
A: Glycosyl hydrolase, family 31/fibronectin type III domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2684
Polymers16,9151
Non-polymers3533
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycosyl hydrolase, family 31/fibronectin type III domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2684
Polymers16,9151
Non-polymers3533
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.300, 84.750, 86.170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-366-

HOH

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Components

#1: Protein Glycosyl hydrolase, family 31/fibronectin type III domain protein


Mass: 16914.762 Da / Num. of mol.: 2 / Fragment: UNP residues 1323-1470
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (bacteria) / Strain: ATCC 13124 / NCTC 8237 / Type A / Gene: CPF_1301 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0TRJ3, UniProt: A0A0H2YST8*PLUS
#2: Sugar ChemComp-NGA / 2-acetamido-2-deoxy-beta-D-galactopyranose / N-acetyl-beta-D-galactosamine / 2-acetamido-2-deoxy-beta-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-D-GALACTOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGalpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-galactopyranosamineCOMMON NAMEGMML 1.0
b-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 352 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.89 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 25% PEG 3350 0.1M BisTris pH 6.5 5% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 29, 2014
RadiationMonochromator: Double crystal Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→38.407 Å / Num. obs: 24623 / % possible obs: 99.9 % / Redundancy: 14 % / Net I/σ(I): 13.7
Reflection shellResolution: 2→2.05 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0.52 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
iMOSFLMdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2→38.407 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 17.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1923 1255 5.11 %
Rwork0.1449 --
obs0.1473 24574 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→38.407 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2322 0 44 352 2718
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072407
X-RAY DIFFRACTIONf_angle_d1.033242
X-RAY DIFFRACTIONf_dihedral_angle_d12.872895
X-RAY DIFFRACTIONf_chiral_restr0.04371
X-RAY DIFFRACTIONf_plane_restr0.003416
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.08010.21411260.14612545X-RAY DIFFRACTION100
2.0801-2.17480.22041230.1442581X-RAY DIFFRACTION100
2.1748-2.28940.19811520.14592530X-RAY DIFFRACTION100
2.2894-2.43280.20761520.14692531X-RAY DIFFRACTION100
2.4328-2.62060.18831470.1552562X-RAY DIFFRACTION100
2.6206-2.88430.19811340.15542594X-RAY DIFFRACTION100
2.8843-3.30140.22661490.14832580X-RAY DIFFRACTION100
3.3014-4.15870.14611460.12622623X-RAY DIFFRACTION100
4.1587-38.41390.19091260.152773X-RAY DIFFRACTION100

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