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Yorodumi- PDB-3c5m: Crystal structure of oligogalacturonate lyase (VPA0088) from Vibr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3c5m | ||||||
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Title | Crystal structure of oligogalacturonate lyase (VPA0088) from Vibrio parahaemolyticus. Northeast Structural Genomics Consortium Target VpR199 | ||||||
Components | Oligogalacturonate lyase | ||||||
Keywords | LYASE / 7 blade-shaped beta-propeller / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Function and homology information oligogalacturonide lyase activity / pectin catabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | Vibrio parahaemolyticus RIMD 2210633 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å | ||||||
Authors | Forouhar, F. / Abashidze, M. / Seetharaman, J. / Janjua, H. / Mao, L. / Xiao, R. / Owens, L.A. / Wang, D. / Baran, M.C. / Acton, T.B. ...Forouhar, F. / Abashidze, M. / Seetharaman, J. / Janjua, H. / Mao, L. / Xiao, R. / Owens, L.A. / Wang, D. / Baran, M.C. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of oligogalacturonate lyase (VPA0088) from Vibrio parahaemolyticus. Authors: Forouhar, F. / Abashidze, M. / Seetharaman, J. / Janjua, H. / Mao, L. / Xiao, R. / Owens, L.A. / Wang, D. / Baran, M.C. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3c5m.cif.gz | 232.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3c5m.ent.gz | 197 KB | Display | PDB format |
PDBx/mmJSON format | 3c5m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3c5m_validation.pdf.gz | 455.1 KB | Display | wwPDB validaton report |
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Full document | 3c5m_full_validation.pdf.gz | 495.8 KB | Display | |
Data in XML | 3c5m_validation.xml.gz | 46.4 KB | Display | |
Data in CIF | 3c5m_validation.cif.gz | 63.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c5/3c5m ftp://data.pdbj.org/pub/pdb/validation_reports/c5/3c5m | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 45687.426 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio parahaemolyticus RIMD 2210633 (bacteria) Species: Vibrio parahaemolyticus / Strain: RIMD 2210633 / Serotype O3:K6 / Gene: VPA0088 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q87K10 #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | AUTHORS STATE THAT ELECTRON DENSITY CLEARLY SHOWS THAT THE RESIDUE AT THE SEQUENCE POSITION 31 IS ...AUTHORS STATE THAT ELECTRON DENSITY CLEARLY SHOWS THAT THE RESIDUE AT THE SEQUENCE POSITION 31 IS NOT VALINE. THE ILE SIDE CHAIN HAS BEEN MODELED ACCORDING TO THE ELECTRON DENSITY AT SEQUENCE POSITION 31. | |
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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: 2.94 Å3/Da / Density % sol: 58.12 % Description: The structure factor file contains Friedel pairs |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Protein solution: 10 mM Tris-HCl pH 7.5, 100 mM NaCl, 5 mM DTT. Reservoir solution: 100 mM MES pH 6.5, 20% PEG 3350, 100 mM Ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 15, 2007 / Details: Mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→30 Å / Num. all: 94903 / Num. obs: 94903 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.3 % / Biso Wilson estimate: 23.8 Å2 / Rmerge(I) obs: 0.126 / Rsym value: 0.105 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.363 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.297 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.6→19.96 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 242133.24 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: The Friedel pairs were used in phasing
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 31.171 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→19.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.69 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 10
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