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Yorodumi- PDB-3vdh: Crystal structure of PbGH5A, a glycoside hydrolase family 5 enzym... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vdh | |||||||||
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Title | Crystal structure of PbGH5A, a glycoside hydrolase family 5 enzyme from Prevotella bryantii B14 | |||||||||
Components | B-1,4-endoglucanase | |||||||||
Keywords | HYDROLASE / 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 / metal ion binding Similarity search - Function | |||||||||
Biological species | Prevotella bryantii (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.62 Å | |||||||||
Authors | Stogios, P.J. / Evdokimova, E. / Egorova, O. / Yim, V. / Joachimiak, A. / Edwards, A.M. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG) | |||||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vdh.cif.gz | 325.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vdh.ent.gz | 268.1 KB | Display | PDB format |
PDBx/mmJSON format | 3vdh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3vdh_validation.pdf.gz | 430.9 KB | Display | wwPDB validaton report |
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Full document | 3vdh_full_validation.pdf.gz | 433.2 KB | Display | |
Data in XML | 3vdh_validation.xml.gz | 34.9 KB | Display | |
Data in CIF | 3vdh_validation.cif.gz | 54.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vd/3vdh ftp://data.pdbj.org/pub/pdb/validation_reports/vd/3vdh | HTTPS FTP |
-Related structure data
Related structure data | 5d9mC 5d9nC 5d9oC 5d9pC 2jeqS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | 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 | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.34 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 22, 2009 / Details: mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 1.6→1.63 Å / Redundancy: 4 % / Mean I/σ(I) obs: 4.67 / Rsym value: 0.443 / % possible all: 61.6 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 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
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Solvent computation | Shrinkage 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 |
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Refinement step | Cycle: LAST / Resolution: 1.62→26.354 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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