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- PDB-2vvp: Crystal structure of Mycobacterium tuberculosis ribose-5-phosphat... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2vvp | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis ribose-5-phosphate isomerase B in complex with its substrates ribose 5-phosphate and ribulose 5-phosphate | ||||||
![]() | RIBOSE-5-PHOSPHATE ISOMERASE B | ||||||
![]() | ISOMERASE / RPIB / RV2465C / RARE SUGAR / CARBOHYDRATE METABOLISM / PENTOSE PHOSPHATE PATHWAY | ||||||
Function / homology | ![]() D-allose catabolic process / ribose-5-phosphate isomerase / ribose-5-phosphate isomerase activity / pentose-phosphate shunt, non-oxidative branch / carbohydrate metabolic process / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kowalinski, E. / Roos, A.K. / Mariano, S. / Salmon, L. / 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 | ![]() | 179.6 KB | Display | ![]() |
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PDB format | ![]() | 144.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2vvoC ![]() 2vvqC ![]() 2vvrC ![]() 1uslS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 17299.514 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q79FD7, UniProt: P9WKD7*PLUS, ribose-5-phosphate isomerase #2: Chemical | ChemComp-R52 / #3: Sugar | ChemComp-5RP / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.5 % / Description: NONE |
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Crystal grow | Details: 20% PEG 3000, 0.1 M TRIS PH 7, 0.2 M CA ACETATE |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 5, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→35 Å / Num. obs: 115358 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 3.6 % / Biso Wilson estimate: 19.8 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 1.65→1.74 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 3 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1USL Resolution: 1.65→34.71 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.501 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.08 / 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: 13.95 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→34.71 Å
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Refine LS restraints |
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