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Yorodumi- PDB-2fps: Crystal structure of the N-terminal domain of E.coli HisB- Apo Ca... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2fps | ||||||
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Title | Crystal structure of the N-terminal domain of E.coli HisB- Apo Ca model. | ||||||
Components | Histidine biosynthesis bifunctional protein hisB | ||||||
Keywords | HYDROLASE / histidinol phosphate phosphatase / HisB / bifunctional enzyme. / Structural Genomics / Bacterial Structure Genomics / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI | ||||||
Function / homology | Function and homology information histidinol-phosphatase / histidinol-phosphatase activity / imidazoleglycerol-phosphate dehydratase / imidazoleglycerol-phosphate dehydratase activity / L-histidine biosynthetic process / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.2 Å | ||||||
Authors | Rangarajan, E.S. / Cygler, M. / Matte, A. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI) | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: Structural snapshots of Escherichia coli histidinol phosphate phosphatase along the reaction pathway. Authors: Rangarajan, E.S. / Proteau, A. / Wagner, J. / Hung, M.N. / Matte, A. / Cygler, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fps.cif.gz | 86.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fps.ent.gz | 63.7 KB | Display | PDB format |
PDBx/mmJSON format | 2fps.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fp/2fps ftp://data.pdbj.org/pub/pdb/validation_reports/fp/2fps | HTTPS FTP |
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-Related structure data
Related structure data | 2fprSC 2fpuC 2fpwC 2fpxC 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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Components on special symmetry positions |
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Details | dimer in asymmetric unit is the biological assembly for the N-terminal domain. |
-Components
#1: Protein | Mass: 20066.730 Da / Num. of mol.: 2 / Fragment: N-terminal domain, Histidinol-phosphatase Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 / Gene: HisB / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9S5G5, histidinol-phosphatase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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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: 2.41 Å3/Da / Density % sol: 48.89 % |
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Crystal grow | Temperature: 293 K / Method: evaporation / pH: 6.5 Details: 30% (w/v) PEG monomethyl ether 550, 0.05M CaCl2, 0.1M Bis-Tris., pH 6.5, EVAPORATION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.7 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 12, 2005 / Details: Mirrors |
Radiation | Monochromator: silicone / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.7 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 17942 / Num. obs: 17045 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rsym value: 0.029 / Net I/σ(I): 39.8 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 19.6 / Rsym value: 0.049 / % possible all: 69.4 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB Entry 2FPR Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.895 / SU B: 5.566 / SU ML: 0.144 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.28 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.493 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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