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- PDB-1bq4: SACCHAROMYCES CEREVISIAE PHOSPHOGLYCERATE MUTASE IN COMPLEX WITH ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1bq4 | ||||||
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Title | SACCHAROMYCES CEREVISIAE PHOSPHOGLYCERATE MUTASE IN COMPLEX WITH BENZENE HEXACARBOXYLATE | ||||||
![]() | PROTEIN (PHOSPHOGLYCERATE MUTASE 1) | ||||||
![]() | ISOMERASE / TRANSFERASE (PHOSPHORYL) / GLYCOLYTIC ENZYME | ||||||
Function / homology | ![]() phosphoglycerate mutase activity / 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity / phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / gluconeogenesis / glycolytic process / mitochondrial intermembrane space / mitochondrial outer membrane / mitochondrion / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Rigden, D.J. / Phillips, S.E.V. / Fothergill-Gilmore, L.A. | ||||||
![]() | ![]() Title: Polyanionic inhibitors of phosphoglycerate mutase: combined structural and biochemical analysis. Authors: Rigden, D.J. / Walter, R.A. / Phillips, S.E. / Fothergill-Gilmore, L.A. #1: ![]() Title: Sulphate Ions Observed in the 2.12 A Structure of a New Crystal Form of S. Cerevisiae Phosphoglycerate Mutase Provide Insights into Understanding the Catalytic Mechanism Authors: Rigden, D.J. / Phillips, S.E.V. / Fothergill-Gilmore, L.A. #2: ![]() Title: The 2.3 Angstroms X-Ray Structure of S.Cerevisiae Phosphoglycerate Mutase Authors: Rigden, D.J. / Alexeev, D. / Phillips, S.E.V. / Fothergill-Gilmore, L.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 193.2 KB | Display | ![]() |
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PDB format | ![]() | 156.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 886.7 KB | Display | ![]() |
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Full document | ![]() | 912.1 KB | Display | |
Data in XML | ![]() | 22.9 KB | Display | |
Data in CIF | ![]() | 33.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1bq3C ![]() 5pgmS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (1, 0.00068, -5.0E-5), Vector: |
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Components
#1: Protein | Mass: 27517.369 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-BHC / | Nonpolymer details | HETEROGEN: BHC MODELLED AS SEMI-IONIZED | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.1 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.65 Details: PROTEIN WAS CRYSTALLISED FROM 22-24% PEG 4000 60MM TRIS-HCL, pH 8.65 | ||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop / Details: Rigden, D.J., (1998) J.Mol.Biol., 276, 449. | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jan 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. obs: 49354 / % possible obs: 63 % / Redundancy: 1.7 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 6 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.254 / Mean I/σ(I) obs: 2.7 / % possible all: 47.5 |
Reflection | *PLUS % possible obs: 63 % |
Reflection shell | *PLUS % possible obs: 47.5 % |
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Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: PDB ENTRY 5PGM Resolution: 2.5→30 Å / Rfactor Rfree error: 0.0051 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0 Details: C-TERMINAL RESIDUES A 235 - A 246, B 236 - B 246, C 236 - C 246 AND D 235 - D 246 ARE NOT VISIBLE IN ELECTRON DENSITY MAP. CLEAVAGE OF SOME OR ALL OF THESE RESIDUES MAY HAVE OCCURRED.
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Displacement parameters | Biso mean: 29.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati d res low obs: 30 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.61 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 29.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.5 Å / Rfactor Rfree: 0.419 / % reflection Rfree: 5 % / Rfactor Rwork: 0.33 |