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Yorodumi- PDB-2vvr: Crystal structure of the H99N mutant of ribose-5-phosphate isomer... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vvr | ||||||
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Title | Crystal structure of the H99N mutant of ribose-5-phosphate isomerase B from E. coli soaked with ribose 5-phosphate | ||||||
Components | RIBOSE-5-PHOSPHATE ISOMERASE B | ||||||
Keywords | ISOMERASE / RPIB / CARBOHYDRATE METABOLISM / PENTOSE PHOSPHATE PATHWAY | ||||||
Function / homology | Function and homology information D-allose 6-phosphate isomerase activity / D-allose catabolic process / ribose-5-phosphate isomerase / ribose-5-phosphate isomerase activity / pentose-phosphate shunt, non-oxidative branch Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Roos, A.K. / Mowbray, S.L. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: D-Ribose-5-Phosphate Isomerase B from Escherichia Coli is Also a Functional D-Allose-6-Phosphate Isomerase, While the Mycobacterium Tuberculosis Enzyme is not. Authors: Roos, A.K. / Mariano, S. / Kowalinski, E. / Salmon, L. / Mowbray, S.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vvr.cif.gz | 173.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vvr.ent.gz | 141.9 KB | Display | PDB format |
PDBx/mmJSON format | 2vvr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vvr_validation.pdf.gz | 455.9 KB | Display | wwPDB validaton report |
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Full document | 2vvr_full_validation.pdf.gz | 459.9 KB | Display | |
Data in XML | 2vvr_validation.xml.gz | 33.8 KB | Display | |
Data in CIF | 2vvr_validation.cif.gz | 48.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vv/2vvr ftp://data.pdbj.org/pub/pdb/validation_reports/vv/2vvr | HTTPS FTP |
-Related structure data
Related structure data | 2vvoC 2vvpC 2vvqC 1nn4S 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 16070.268 Da / Num. of mol.: 6 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K12 / Plasmid: PBAD/TOPO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TOP10 / References: UniProt: P37351, ribose-5-phosphate isomerase #2: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, HIS 99 TO ASN ENGINEERED RESIDUE IN CHAIN B, HIS 99 TO ASN ...ENGINEERED | Sequence details | H99N MUTANT | |
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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: 2.11 Å3/Da / Density % sol: 41.7 % / Description: NONE |
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Crystal grow | Details: 20% PEG 3350, 0.1 M MES PH6 |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.94 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 5, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.94 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→40.49 Å / Num. obs: 50635 / % possible obs: 99.9 % / Observed criterion σ(I): 5.8 / Redundancy: 3.6 % / Biso Wilson estimate: 19.1 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 5.8 / % possible all: 99.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1NN4 Resolution: 2.1→40 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.903 / SU B: 4.579 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.236 / ESU R Free: 0.193 / 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 mean: 13.77 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→40 Å
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Refine LS restraints |
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