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Yorodumi- PDB-3vmw: Crystal structure of pectate lyase Bsp165PelA from Bacillus sp. N... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vmw | |||||||||
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Title | Crystal structure of pectate lyase Bsp165PelA from Bacillus sp. N165 in complex with trigalacturonate | |||||||||
Components | Pectate lyase | |||||||||
Keywords | LYASE / Polysaccharide Lyase Family 1 / pectate lyase / beta-helix / pectolytic / polygalacturonate | |||||||||
Function / homology | Function and homology information pectate lyase activity / polysaccharide catabolic process / extracellular region Similarity search - Function | |||||||||
Biological species | Bacillus (Bacillus rRNA group 1) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Zheng, Y. / Huang, C.H. / Liu, W. / Ko, T.P. / Xue, Y. / Zhou, C. / Zhang, G. / Guo, R.T. / Ma, Y. | |||||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2012 Title: Crystal structure and substrate-binding mode of a novel pectate lyase from alkaliphilic Bacillus sp. N16-5. Authors: Zheng, Y. / Huang, C.H. / Liu, W. / Ko, T.P. / Xue, Y. / Zhou, C. / Guo, R.T. / Ma, Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vmw.cif.gz | 149.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vmw.ent.gz | 116.6 KB | Display | PDB format |
PDBx/mmJSON format | 3vmw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3vmw_validation.pdf.gz | 832.9 KB | Display | wwPDB validaton report |
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Full document | 3vmw_full_validation.pdf.gz | 836.9 KB | Display | |
Data in XML | 3vmw_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | 3vmw_validation.cif.gz | 22.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vm/3vmw ftp://data.pdbj.org/pub/pdb/validation_reports/vm/3vmw | HTTPS FTP |
-Related structure data
Related structure data | 3vmvSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 35979.137 Da / Num. of mol.: 1 / Fragment: catalytic domain (UNP RESIDUES 37-362) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus (Bacillus rRNA group 1) / Strain: N16-5 / Gene: GU088530, pelA / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: D0VP31, pectate lyase | ||
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#2: Polysaccharide | alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid Source method: isolated from a genetically manipulated source | ||
#3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.22 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.18M Li2SO4, 0.085M Tris-HCl, pH 8.5, 24%, PEG 4000, 15% v/v Glycerol anhydrous , VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 20, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→25 Å / Num. obs: 28061 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 10 % / Rmerge(I) obs: 0.05 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.223 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3VMV Resolution: 1.9→24.52 Å / SU ML: 0.22 / σ(F): 1.35 / Phase error: 17.88 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.739 Å2 / ksol: 0.386 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.9→24.52 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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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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