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Yorodumi- PDB-2fpx: Crystal Structure of the N-terminal Domain of E.coli HisB- Sulfat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2fpx | ||||||
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Title | Crystal Structure of the N-terminal Domain of E.coli HisB- Sulfate complex. | ||||||
Components | Histidine biosynthesis bifunctional protein hisB | ||||||
Keywords | HYDROLASE / Histidinol phosphate phosphatase / HisB / bifunctional enzyme. / Structural 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: 1.8 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 | 2fpx.cif.gz | 91.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fpx.ent.gz | 66.9 KB | Display | PDB format |
PDBx/mmJSON format | 2fpx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fp/2fpx ftp://data.pdbj.org/pub/pdb/validation_reports/fp/2fpx | HTTPS FTP |
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-Related structure data
Related structure data | 2fprSC 2fpsC 2fpuC 2fpwC 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 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 | ChemComp-SO4 / | #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: 2.53 Å3/Da / Density % sol: 51.3 % |
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Crystal grow | Temperature: 280 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 25%(w/v) PEG 3350, 0.2M MgSO4, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 280K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 18, 2005 / Details: mirrors |
Radiation | Monochromator: silicone / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 34959 / Num. obs: 34959 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rsym value: 0.067 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.9 / Rsym value: 0.343 / % possible all: 82.6 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB Entry 2FPR Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.196 / SU ML: 0.071 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.796 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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