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Yorodumi- PDB-1bq3: SACCHAROMYCES CEREVISIAE PHOSPHOGLYCERATE MUTASE IN COMPLEX WITH ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1bq3 | ||||||
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Title | SACCHAROMYCES CEREVISIAE PHOSPHOGLYCERATE MUTASE IN COMPLEX WITH INOSITOL HEXAKISPHOSPHATE | ||||||
Components | PROTEIN (PHOSPHOGLYCERATE MUTASE 1) | ||||||
Keywords | ISOMERASE / TRANSFERASE (PHOSPHORYL) / GLYCOLYTIC ENZYME | ||||||
Function / homology | Function and homology information 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 | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / OTHER / Resolution: 2.7 Å | ||||||
Authors | Rigden, D.J. / Phillips, S.E.V. / Fothergill-Gilmore, L.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1999 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: Journal: J.Mol.Biol. / Year: 1999 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.P. / Fothergill-Gilmore, L.A. #2: Journal: J.Mol.Biol. / Year: 1998 Title: The 2.3 Angstroms X-Ray Structure of S.Cerevisiae Phosphoglycerate Mutase Authors: Rigden, D.J. / Alexeev, D. / Phillips, S.E.V.P. / Fothergill-Gilmore, L.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bq3.cif.gz | 191.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bq3.ent.gz | 154.6 KB | Display | PDB format |
PDBx/mmJSON format | 1bq3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bq/1bq3 ftp://data.pdbj.org/pub/pdb/validation_reports/bq/1bq3 | HTTPS FTP |
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-Related structure data
Related structure data | 1bq4C 5pgmS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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, 0.00014, 0.00205), Vector: |
-Components
#1: Protein | Mass: 27517.369 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Cellular location: CYTOPLASM / Strain: S150-GPM::HIS3 / References: UniProt: P00950, EC: 5.4.2.1 #2: Chemical | #3: Chemical | ChemComp-SO4 / Nonpolymer details | HETEROGEN: IHP MODELLED AS SEMI-IONIZED | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Oct 15, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→30 Å / Num. obs: 41238 / % possible obs: 66 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.189 / Mean I/σ(I) obs: 3.9 / % possible all: 54.6 |
Reflection | *PLUS % possible obs: 66 % |
Reflection shell | *PLUS % possible obs: 54.6 % |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: PDB ENTRY 5PGM Resolution: 2.7→30 Å / Rfactor Rfree error: 0.0052 / 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: 18.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati d res low obs: 30 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→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: 2.7→2.82 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.2 / Rfactor Rfree: 0.24 / Rfactor Rwork: 0.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 18.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.7 Å / Rfactor Rfree: 0.317 / % reflection Rfree: 5 % / Rfactor Rwork: 0.279 |