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Yorodumi- PDB-2fpw: Crystal Structure of the N-terminal Domain of E.coli HisB- Phosph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2fpw | ||||||
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Title | Crystal Structure of the N-terminal Domain of E.coli HisB- Phosphoaspartate intermediate. | ||||||
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 / amino acid biosynthetic process / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.75 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 | 2fpw.cif.gz | 90.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fpw.ent.gz | 66.5 KB | Display | PDB format |
PDBx/mmJSON format | 2fpw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2fpw_validation.pdf.gz | 440.7 KB | Display | wwPDB validaton report |
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Full document | 2fpw_full_validation.pdf.gz | 442.1 KB | Display | |
Data in XML | 2fpw_validation.xml.gz | 19.4 KB | Display | |
Data in CIF | 2fpw_validation.cif.gz | 29.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fp/2fpw ftp://data.pdbj.org/pub/pdb/validation_reports/fp/2fpw | HTTPS FTP |
-Related structure data
Related structure data | 2fprSC 2fpsC 2fpuC 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 is asymmetric unit is the biological assembly for the N-terminal domain. |
-Components
#1: Protein | Mass: 20146.711 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: 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: 2.44 Å3/Da / Density % sol: 49.69 % |
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Crystal grow | Temperature: 293 K / Method: evaporation / pH: 6.5 Details: 30% (w/v) PEG monomethylether 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: 1.1 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: 1.75→50 Å / Num. all: 36862 / Num. obs: 36862 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rsym value: 0.07 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 7.1 / Rsym value: 0.25 / % possible all: 92 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB Entry 2FPR Resolution: 1.75→50 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.932 / SU B: 1.927 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.112 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.561 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.795 Å / Total num. of bins used: 20
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