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- PDB-2vvr: Crystal structure of the H99N mutant of ribose-5-phosphate isomer... -
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Open data
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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 | ||||||
![]() | RIBOSE-5-PHOSPHATE ISOMERASE B | ||||||
![]() | ISOMERASE / RPIB / CARBOHYDRATE METABOLISM / PENTOSE PHOSPHATE PATHWAY | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Roos, A.K. / Mowbray, S.L. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 173.9 KB | Display | ![]() |
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PDB format | ![]() | 141.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 455.9 KB | Display | ![]() |
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Full document | ![]() | 459.9 KB | Display | |
Data in XML | ![]() | 33.8 KB | Display | |
Data in CIF | ![]() | 48.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2vvoC ![]() 2vvpC ![]() 2vvqC ![]() 1nn4S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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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.) ![]() ![]() ![]() ![]() #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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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