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Yorodumi- PDB-1vey: Crystal Structure of Peptide Deformylase from Leptospira Interrog... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vey | ||||||
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Title | Crystal Structure of Peptide Deformylase from Leptospira Interrogans (LiPDF) at pH7.0 | ||||||
Components | Peptide deformylase | ||||||
Keywords | HYDROLASE / closed conformation / HEPES | ||||||
Function / homology | Function and homology information co-translational protein modification / peptide deformylase / peptide deformylase activity / translation / metal ion binding Similarity search - Function | ||||||
Biological species | Leptospira interrogans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | ||||||
Authors | Zhou, Z. / Song, X. / Li, Y. / Gong, W. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: Novel conformational states of peptide deformylase from pathogenic bacterium Leptospira interrogans: implications for population shift Authors: Zhou, Z. / Song, X. / Gong, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vey.cif.gz | 79.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vey.ent.gz | 60.1 KB | Display | PDB format |
PDBx/mmJSON format | 1vey.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1vey_validation.pdf.gz | 446.1 KB | Display | wwPDB validaton report |
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Full document | 1vey_full_validation.pdf.gz | 459.3 KB | Display | |
Data in XML | 1vey_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | 1vey_validation.cif.gz | 20.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ve/1vey ftp://data.pdbj.org/pub/pdb/validation_reports/ve/1vey | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | The biological unit 1 is generated by chain A (x,y,z (1_555),1-y,1-x,1/2-z (8_665)) / The biological unit 2 is generated by chain B (x,y,z (1_555),1+y,-1+x,-z (7_645)) |
-Components
#1: Protein | Mass: 20274.117 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leptospira interrogans (bacteria) / Plasmid: pET22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q93LE9, peptide deformylase #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: 4.34 Å3/Da / Density % sol: 70 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 4m formate sodium, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.54 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 5, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→100 Å / Num. all: 11460 / Num. obs: 10617 / % possible obs: 83.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 3.3→3.51 Å / % possible all: 86 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Highest resolution: 3.3 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Highest resolution: 3.3 Å
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Refine LS restraints |
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