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Yorodumi- PDB-3env: Substrate and inhibitor complexes of ribose 5-phosphate isomerase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3env | |||||||||
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Title | Substrate and inhibitor complexes of ribose 5-phosphate isomerase from Vibrio vulnificus YJ016 | |||||||||
Components | Ribose-5-phosphate isomerase A | |||||||||
Keywords | ISOMERASE / ribose 5-phosphate / arabinose 5-phosphate | |||||||||
Function / homology | Function and homology information ribose-5-phosphate isomerase / ribose-5-phosphate isomerase activity / pentose-phosphate shunt, non-oxidative branch Similarity search - Function | |||||||||
Biological species | Vibrio vulnificus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Min, K. / Kwon, T.H. / Kim, T.G. | |||||||||
Citation | Journal: Mol.Cells / Year: 2009 Title: Crystal structures of substrate and inhibitor complexes of ribose 5-phosphate isomerase A from Vibrio vulnificus YJ016 Authors: Kim, T.G. / Kwon, T.H. / Min, K. / Dong, M.S. / Park, Y.I. / Ban, C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3env.cif.gz | 93 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3env.ent.gz | 70 KB | Display | PDB format |
PDBx/mmJSON format | 3env.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/en/3env ftp://data.pdbj.org/pub/pdb/validation_reports/en/3env | HTTPS FTP |
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-Related structure data
Related structure data | 3enqSC 3enwC C: citing same article (ref.) S: Starting model for refinement |
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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: 24672.213 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio vulnificus (bacteria) / Strain: YJ016 / Gene: rpiA / Plasmid: pET28aTEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7MHL9, ribose-5-phosphate isomerase #2: Sugar | #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: 2.2 Å3/Da / Density % sol: 44.13 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.5 Details: 8% PEG4000, 0.05M succinate, pH4.0, 0.18M ammonium sulfate, 10mM arabinose 5-phosphate, pH7.5, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 28464 / Num. obs: 28464 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ENQ Resolution: 2→25 Å / Cor.coef. Fo:Fc: 0.791 / Cor.coef. Fo:Fc free: 0.67 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 6.876 / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.254 / ESU R Free: 0.242 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 34.48 Å2 / Biso mean: 7.302 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 2→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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