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- PDB-1h2f: BACILLUS STEAROTHERMOPHILUS PHOE (previously known as yhfr) in co... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1h2f | ||||||
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Title | BACILLUS STEAROTHERMOPHILUS PHOE (previously known as yhfr) in complex with trivanadate | ||||||
![]() | PHOSPHATASE | ||||||
![]() | HYDROLASE / BROAD SPECIFICITY PHOSPHATASE / DPGM HOMOLOG | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Rigden, D.J. / Littlejohn, J.E. / Jedrzejas, M.J. | ||||||
![]() | ![]() Title: Structures of Phosphate and Trivanadate Complexes of Bacillus Stearothermophilus Phosphatase Phoe: Structural and Functional Analysis in the Cofactor-Dependent Phosphoglycerate Mutase Superfamily Authors: Rigden, D.J. / Littlejohn, J.E. / Henderson, K. / Jedrzejas, M.J. #1: ![]() 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. #2: 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 56 KB | Display | ![]() |
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PDB format | ![]() | 44.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 23647.676 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-VA3 / |
#3: Chemical | ChemComp-PO4 / |
#4: Water | ChemComp-HOH / |
Compound details | THE SWISSPROT ENTRY Q9ALU0 IDENTIFIES THIS PROTEIN AS A PHOSPHOGLYCERATE MUTASE. THE PROTEIN ...THE SWISSPROT ENTRY Q9ALU0 IDENTIFIES |
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: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.3 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.5 Details: 15 % ETHYLENE GLYCOL, 85 MM SODIUM CACODYLATE PH 4.5 | |||||||||||||||||||||||||||||||||||||||||||||||||
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: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 15, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 17334 / % possible obs: 95.2 % / Redundancy: 4.9 % / Biso Wilson estimate: 29.6 Å2 / Rmerge(I) obs: 0.155 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.554 / Mean I/σ(I) obs: 2.1 / % possible all: 88.2 |
Reflection | *PLUS Lowest resolution: 50 Å |
Reflection shell | *PLUS % possible obs: 88.2 % / Mean I/σ(I) obs: 1.4 |
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Processing
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Refinement | Method to determine structure: OTHER / Resolution: 2→50 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1636651.82 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: CRYSTAL WAS EXPOSED TO 50MM AMMONIUM VANADATE, 30% ETHYLENE GLYCOL, 20MM SODIUM ACETATE PH 5.0 FOR 3 DAYS BEFORE DATA COLLECTION.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.1339 Å2 / ksol: 0.307577 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.07 Å / Rfactor Rfree error: 0.042 / Total num. of bins used: 10
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Xplor file |
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Refinement | *PLUS Lowest resolution: 50 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.358 / Rfactor Rwork: 0.338 / Num. reflection Rwork: 1942 |