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Yorodumi- PDB-1vev: Crystal structure of peptide deformylase from Leptospira Interrog... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vev | ||||||
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Title | Crystal structure of peptide deformylase from Leptospira Interrogans (LiPDF) at pH6.5 | ||||||
Components | Peptide deformylase | ||||||
Keywords | HYDROLASE / closed conformation / MES | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 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 | 1vev.cif.gz | 85.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vev.ent.gz | 63.8 KB | Display | PDB format |
PDBx/mmJSON format | 1vev.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1vev_validation.pdf.gz | 459.6 KB | Display | wwPDB validaton report |
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Full document | 1vev_full_validation.pdf.gz | 468.4 KB | Display | |
Data in XML | 1vev_validation.xml.gz | 18.3 KB | Display | |
Data in CIF | 1vev_validation.cif.gz | 25.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ve/1vev ftp://data.pdbj.org/pub/pdb/validation_reports/ve/1vev | HTTPS FTP |
-Related structure data
Related structure data | 1sv2SC 1szzC 1veyC 1vezC 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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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: 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: 4.34 Å3/Da / Density % sol: 70 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 4M formate sodium, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1.2 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 1, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2 Å / Relative weight: 1 |
Reflection | Resolution: 2.51→43.91 Å / Num. all: 24689 / Num. obs: 21663 / % possible obs: 87.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.5→2.66 Å / % possible all: 75.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB id 1SV2 Resolution: 2.51→43.91 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.51→43.91 Å
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Refine LS restraints |
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