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Yorodumi- PDB-5cvq: Structure of Xoo1075, a peptide deformylase from Xanthomonas oryz... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5cvq | ||||||
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Title | Structure of Xoo1075, a peptide deformylase from Xanthomonas oryzae pv oryzae, in complex with actinonin | ||||||
Components | Peptide deformylase | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / peptide deformylase / Xanthomonas / actinonin / metallopeptidase / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information peptide deformylase / peptide deformylase activity / translation / metal ion binding Similarity search - Function | ||||||
Biological species | Xanthomonas oryzae pv. oryzae KACC10331 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Ngo, H.P.T. / Kang, L.W. | ||||||
Citation | Journal: To Be Published Title: Structure of Xoo1075, a peptide deformylase from Xanthomonas oryzae pv oryzae, in complex with actinonin Authors: Ngo, H.P.T. / Kang, L.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5cvq.cif.gz | 50.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5cvq.ent.gz | 34 KB | Display | PDB format |
PDBx/mmJSON format | 5cvq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cv/5cvq ftp://data.pdbj.org/pub/pdb/validation_reports/cv/5cvq | HTTPS FTP |
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-Related structure data
Related structure data | 5e5dS S: Starting model for refinement |
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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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-Components
#1: Protein | Mass: 19097.656 Da / Num. of mol.: 1 / Fragment: UNP residues 42-212 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xanthomonas oryzae pv. oryzae KACC10331 (bacteria) Strain: KACC10331 / Gene: def, XOO1075 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5H3Z2, peptide deformylase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-ACT / | #4: Chemical | ChemComp-BB2 / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.45 Å3/Da / Density % sol: 64.4 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.05M Cadmium sulfate, 0.1M HEPES, 2.0M Sodium acetate trihydrate, pH 7.5 PH range: 7.0-8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.99 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 22, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 13892 / % possible obs: 93.5 % / Redundancy: 6.6 % / Net I/σ(I): 9.2 |
Reflection shell | Highest resolution: 2.2 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.672 / Mean I/σ(I) obs: 2.1 / % possible all: 91.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5E5D Resolution: 2.5→27.84 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.923 / SU B: 6.395 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.264 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.069 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→27.84 Å
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Refine LS restraints |
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