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- PDB-1e59: E.coli cofactor-dependent phosphoglycerate mutase complexed with ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1.0E+59 | ||||||
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Title | E.coli cofactor-dependent phosphoglycerate mutase complexed with vanadate | ||||||
![]() | PHOSPHOGLYCERATE MUTASE | ||||||
![]() | ISOMERASE / INHIBITOR / VANDATE / GLYCOLYSIS AND GLUCONEOGENESIS / PHOSPHOGLYCERATE MUTASE | ||||||
Function / homology | ![]() 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity / phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / canonical glycolysis / guanosine tetraphosphate binding / gluconeogenesis / protein homodimerization activity / ATP binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bond, C.S. / Hunter, W.N. | ||||||
![]() | ![]() Title: Mechanistic Implications for Escherichia Coli Cofactor-Dependent Phosphoglycerate Mutase Based on the High-Resolution Crystal Structure of a Vanadate Complex. Authors: Bond, C.S. / White, M. / Hunter, W.N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 122.8 KB | Display | ![]() |
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PDB format | ![]() | 94.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 791.9 KB | Display | ![]() |
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Full document | ![]() | 793.2 KB | Display | |
Data in XML | ![]() | 13.6 KB | Display | |
Data in CIF | ![]() | 20.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1e58S 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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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 28465.195 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P31217, UniProt: P62707*PLUS, EC: 5.4.2.1 |
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#2: Chemical | ChemComp-VO3 / |
#3: Chemical | ChemComp-CL / |
#4: Water | ChemComp-HOH / |
Compound details | CATALYTIC ACTIVITY: 2-PHOSPHOGLYCERATE + 2,3-DIPHOSPHOGLYCERATE = 3-PHOSPHOGLYCERATE + 2,3- ...CATALYTIC ACTIVITY: 2-PHOSPHOGLY |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 51 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.5 Details: 100 MM TRIS-HCL (PH 8.0), 200 MM LI2SO4, 20% PEG 4000, 100 MM NAVO3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Date: Sep 15, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.89 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→30 Å / Num. obs: 68073 / % possible obs: 96.6 % / Redundancy: 4 % / Rsym value: 0.079 / Net I/σ(I): 17 |
Reflection shell | Resolution: 1.3→1.31 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.401 / % possible all: 99.9 |
Reflection | *PLUS Redundancy: 3.1 % / Rmerge(I) obs: 0.079 |
Reflection shell | *PLUS % possible obs: 99.9 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.401 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1E58 Resolution: 1.3→30 Å / Num. parameters: 20185 / Num. restraintsaints: 24690 / Cross valid method: FREE R-VALUE / σ(F): 0 StereochEM target val spec case: VO3 VALUES EXTRACTED FROM CSDS Stereochemistry target values: ENGH AND HUBER
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 4 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2210.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→30 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rwork: 0.1552 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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