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- PDB-1rii: Crystal structure of phosphoglycerate mutase from M. Tuberculosis -
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Open data
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Basic information
Entry | Database: PDB / ID: 1rii | ||||||
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Title | Crystal structure of phosphoglycerate mutase from M. Tuberculosis | ||||||
![]() | 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase | ||||||
![]() | ISOMERASE / Phosphoglyerate Mutase / SH3 Domain Binding / Structural genomics / TBSGC / Protein Structure Initiative / PSI / TB Structural Genomics Consortium | ||||||
Function / homology | ![]() 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity / phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / gluconeogenesis / glycolytic process / protein-containing complex / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mueller, P. / Sawaya, M.R. / Chan, S. / Wu, Y. / Pashkova, I. / Perry, J. / Eisenberg, D. / TB Structural Genomics Consortium (TBSGC) | ||||||
![]() | ![]() Title: The 1.70 angstroms X-ray crystal structure of Mycobacterium tuberculosis phosphoglycerate mutase. Authors: Muller, P. / Sawaya, M.R. / Pashkov, I. / Chan, S. / Nguyen, C. / Wu, Y. / Perry, L.J. / Eisenberg, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 202.8 KB | Display | ![]() |
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PDB format | ![]() | 160.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 477.9 KB | Display | ![]() |
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Full document | ![]() | 496.7 KB | Display | |
Data in XML | ![]() | 41.2 KB | Display | |
Data in CIF | ![]() | 57.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5pgmS S: Starting model for refinement |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Details | The biological assembly is the homotetramer formed by the chains A, B, C and D which forms the asymmetric unit. |
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Components
#1: Protein | Mass: 28999.678 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: GPMA, GPM, PGM, GPM1, RV0489, MT0508, MTCY20G9.15, MB0499 Plasmid: pET22b / Production host: ![]() ![]() References: UniProt: P0A5R6, UniProt: P9WIC9*PLUS, EC: 5.4.2.1 #2: Chemical | ChemComp-GOL / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 45.79 % |
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Crystal grow | Temperature: 298 K / pH: 7 Details: 15% PEG 3350, 0.1M magnesium chloride, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 7.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 11, 2003 |
Radiation | Monochromator: DOUBLE CRYSTAL SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→58.37 Å / Num. obs: 111293 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 21.33 Å2 / Rsym value: 0.0699 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 1.7→1.8 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 3.2 / Rsym value: 0.4548 / % possible all: 91.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 5PGM Resolution: 1.7→58.37 Å / Num. parameters: 31673 / Num. restraintsaints: 31045 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH & HUBER Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56. HYDROGENS HAVE BEEN ADDED AT GEOMETRICALLY CALCULATED POSITIONS AND REFINED USING A RIDING MODEL.
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Solvent computation | Solvent model: Bulk solvent was treated following the Babinet-Principle refining two parameters, using the SWAT command in SHELXL. | |||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.8 Å2 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 11 / Occupancy sum hydrogen: 6617 / Occupancy sum non hydrogen: 7846 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→58.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.8 Å /
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