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- PDB-3vdh: Crystal structure of PbGH5A, a glycoside hydrolase family 5 enzym... -

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Basic information

Entry
Database: PDB / ID: 3vdh
TitleCrystal structure of PbGH5A, a glycoside hydrolase family 5 enzyme from Prevotella bryantii B14
ComponentsB-1,4-endoglucanase
KeywordsHYDROLASE / ENDO-BETA-GLUCANASE/ENDO-XYLOGLUCANASE / GLYCOSYL HYDROLASE FAMILY 5 / MIXED ALPHA-BETA / TIM BARREL / STRUCTURAL GENOMICS / PSI-BIOLOGY / PROTEIN STRUCTURE INITIATIVE / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG
Function / homology
Function and homology information


substituted mannan metabolic process / mannan endo-1,4-beta-mannosidase activity / polysaccharide catabolic process / metal ion binding
Similarity search - Function
Glycoside hydrolase family 26 / Glycosyl hydrolase family 26 / Secretion system C-terminal sorting domain / Glycosyl hydrolase family 26 domain / Glycosyl hydrolases family 26 (GH26) domain profile. / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel ...Glycoside hydrolase family 26 / Glycosyl hydrolase family 26 / Secretion system C-terminal sorting domain / Glycosyl hydrolase family 26 domain / Glycosyl hydrolases family 26 (GH26) domain profile. / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesPrevotella bryantii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsStogios, P.J. / Evdokimova, E. / Egorova, O. / Yim, V. / Joachimiak, A. / Edwards, A.M. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structure-Function Analysis of a Mixed-linkage beta-Glucanase/Xyloglucanase from the Key Ruminal Bacteroidetes Prevotella bryantii B14.
Authors: McGregor, N. / Morar, M. / Fenger, T.H. / Stogios, P. / Lenfant, N. / Yin, V. / Xu, X. / Evdokimova, E. / Cui, H. / Henrissat, B. / Savchenko, A. / Brumer, H.
History
DepositionJan 5, 2012Deposition site: RCSB / Processing site: RCSB
SupersessionJan 18, 2012ID: 3L55
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2015Group: Other
Revision 1.2Nov 4, 2015Group: Database references
Revision 1.3Dec 23, 2015Group: Database references
Revision 1.4Feb 17, 2016Group: Database references
Revision 1.5Jun 22, 2016Group: Structure summary
Revision 1.6Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.7Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.8Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: B-1,4-endoglucanase
B: B-1,4-endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,1945
Polymers80,0882
Non-polymers1063
Water16,430912
1
A: B-1,4-endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1153
Polymers40,0441
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: B-1,4-endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0792
Polymers40,0441
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.908, 85.254, 74.556
Angle α, β, γ (deg.)90.00, 109.15, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein B-1,4-endoglucanase


Mass: 40044.039 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Prevotella bryantii (bacteria) / Plasmid: PET101-11079 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O06842
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 912 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.17 Å3/Da / Density % sol: 43.34 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M CALCIUM ACETATE HYDRATE, 0.1M SODIUM CACODYLATE PH 6.5, 18% PEG 8K, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 22, 2009 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 83351 / % possible obs: 84 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 3.4 % / Rsym value: 0.039 / Net I/σ(I): 38.95
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 4 % / Mean I/σ(I) obs: 4.67 / Rsym value: 0.443 / % possible all: 61.6

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2JEQ

2jeq


Resolution: 1.62→26.354 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.22 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.1993 1951 2.46 %random
Rwork0.1512 ---
obs0.1524 79400 91.45 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.549 Å2 / ksol: 0.354 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.5858 Å20 Å2-5.176 Å2
2--3.2826 Å20 Å2
3----0.6802 Å2
Refinement stepCycle: LAST / Resolution: 1.62→26.354 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5439 0 3 912 6354
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015645
X-RAY DIFFRACTIONf_angle_d1.2227703
X-RAY DIFFRACTIONf_dihedral_angle_d13.0941987
X-RAY DIFFRACTIONf_chiral_restr0.086829
X-RAY DIFFRACTIONf_plane_restr0.0061005
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.67790.31611820.29396976X-RAY DIFFRACTION84
1.6779-1.74510.28471950.24237580X-RAY DIFFRACTION89
1.7451-1.82450.24651910.19747565X-RAY DIFFRACTION90
1.8245-1.92060.22991890.16537660X-RAY DIFFRACTION91
1.9206-2.04090.24771910.15447694X-RAY DIFFRACTION91
2.0409-2.19840.17921950.14097781X-RAY DIFFRACTION92
2.1984-2.41950.21842030.13647892X-RAY DIFFRACTION93
2.4195-2.76930.19051930.14388042X-RAY DIFFRACTION94
2.7693-3.48780.18682000.14068056X-RAY DIFFRACTION95
3.4878-26.35710.17032120.13878203X-RAY DIFFRACTION95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.69810.09221.30660.8412-0.35581.4341-0.19340.54520.2443-0.10690.0732-0.1035-0.080.58380.06880.108-0.0850.01690.3170.04770.1081.178536.96749.4175
21.85410.11011.0961.701-0.21652.33930.08890.0867-0.1398-0.03410.09170.10810.181-0.0614-0.17170.0918-0.0218-0.010.1151-0.00140.1164-12.626826.066115.4509
31.5547-0.39290.87831.1774-0.55780.65320.4270.6481-0.6428-0.22240.0735-0.030.71930.5269-0.29490.33250.1085-0.12970.2628-0.15950.2944-1.654514.828511.9902
41.33910.13570.79481.51980.06151.61810.0585-0.1319-0.01280.0331-0.01880.1436-0.0005-0.0662-0.04410.08570.00980.00690.1169-0.00680.11390.305322.959749.3311
51.50090.10760.32590.8841-0.14082.268-0.01050.00730.10380.0363-0.0792-0.0705-0.30920.38530.05120.1127-0.0319-0.02250.1681-0.00590.13613.01231.417847.2832
61.27690.0479-0.01091.84540.18931.35390.12030.1126-0.119-0.0436-0.0256-0.21450.22320.4869-0.11130.13270.0883-0.03110.2911-0.0260.183817.742315.991838.7742
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 7:206
2X-RAY DIFFRACTION2chain A and resid 207:294
3X-RAY DIFFRACTION3chain A and resid 295:353
4X-RAY DIFFRACTION4chain B and resid 6:179
5X-RAY DIFFRACTION5chain B and resid 180:294
6X-RAY DIFFRACTION6chain B and resid 295:353

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