+Open data
-Basic information
Entry | Database: PDB / ID: 1ebb | ||||||
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Title | Bacillus stearothermophilus YhfR | ||||||
Components | PHOSPHATASE | ||||||
Keywords | HYDROLASE / BROAD SPECIFICITY PHOSPHATASE / DPGM HOMOLOG | ||||||
Function / homology | Phosphoglycerate mutase family / Phosphoglycerate mutase-like / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / Histidine phosphatase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Phosphoglycerate mutase Function and homology information | ||||||
Biological species | BACILLUS STEAROTHERMOPHILUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Rigden, D.J. / Jedrzejas, M.J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: Structure and Mechanism of Action of a Cofactor-Dependent Phosphoglycerate Mutase Homolog from Bacillus Stearothermophilus with Broad Specificity Phosphatase Activity. Authors: Rigden, D.J. / Mello, L.V. / Setlow, P. / Jedrzejas, M.J. #1: Journal: Protein Sci. / Year: 2001 Title: A Cofactor-Dependent Phosphoglycerate Mutase Homolog from Bacillus Stearothermophilus is Actually a Broad Specificity Phosphatase Authors: Rigden, D.J. / Bagyan, I. / Lamani, E. / Setlow, P. / Jedrzejas, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ebb.cif.gz | 56.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ebb.ent.gz | 40.8 KB | Display | PDB format |
PDBx/mmJSON format | 1ebb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eb/1ebb ftp://data.pdbj.org/pub/pdb/validation_reports/eb/1ebb | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23062.006 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACILLUS STEAROTHERMOPHILUS (bacteria) / Plasmid: PS3297 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9ALU0 | ||||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | THE SWISSPROT ENTRY Q9ALU0 IDENTIFIES THIS PROTEIN AS A PHOSPHOGLYCERATE MUTASE. THE PROTEIN ...THE SWISSPROT ENTRY Q9ALU0 IDENTIFIES | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8 Details: 45 % POLYETHYLENE GLYCOL 4,000, 120 MM LITHIUM SULFATE, 20 MM TRIS.HCL BUFFER, PH 8.0 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / pH: 7.4 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1.1 |
Detector | Type: OXFORD / Detector: CCD / Date: Jan 15, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→45.83 Å / Num. obs: 11896 / % possible obs: 99.5 % / Redundancy: 12.2 % / Biso Wilson estimate: 33.2 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 2.3→2.4 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.706 / Mean I/σ(I) obs: 1.3 / % possible all: 98.8 |
Reflection | *PLUS Lowest resolution: 50 Å |
Reflection shell | *PLUS % possible obs: 98.8 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 1TIP, 5PGM +HOMOLOGY MODEL Resolution: 2.3→45.83 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 1587969.35 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.5009 Å2 / ksol: 0.365671 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→45.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.4 Å / Rfactor Rfree error: 0.041 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 50 Å / Rfactor obs: 0.23 / Rfactor Rwork: 0.23 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.337 |