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Yorodumi- PDB-5e5d: Native structure of Xoo1075, a peptide deformylase from Xanthomon... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5e5d | |||||||||
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Title | Native structure of Xoo1075, a peptide deformylase from Xanthomonas oryzae pv. oryzae | |||||||||
Components | Peptide deformylase | |||||||||
Keywords | HYDROLASE / peptide deformylase / metal binding protein | |||||||||
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: 2.6 Å | |||||||||
Authors | Ngo, H.P.T. / Kang, L.W. | |||||||||
Citation | Journal: To Be Published Title: Native structure of Xoo1075, a peptide deformylase from Xanthomonas oryzae pv. oryzae 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 | 5e5d.cif.gz | 53.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5e5d.ent.gz | 35.6 KB | Display | PDB format |
PDBx/mmJSON format | 5e5d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5e5d_validation.pdf.gz | 426.4 KB | Display | wwPDB validaton report |
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Full document | 5e5d_full_validation.pdf.gz | 428.7 KB | Display | |
Data in XML | 5e5d_validation.xml.gz | 10 KB | Display | |
Data in CIF | 5e5d_validation.cif.gz | 13.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e5/5e5d ftp://data.pdbj.org/pub/pdb/validation_reports/e5/5e5d | HTTPS FTP |
-Related structure data
Related structure data | 1sv2S 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: 23830.295 Da / Num. of mol.: 1 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: 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: 2.8 Å3/Da / Density % sol: 56.14 % |
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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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 27, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 9011 / % possible obs: 96.9 % / Redundancy: 9.6 % / Net I/σ(I): 22.5 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 6.6 / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1sv2 Resolution: 2.6→30.4 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.911 / SU B: 8.047 / SU ML: 0.173 / Cross valid method: THROUGHOUT / ESU R: 0.368 / ESU R Free: 0.265 / 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: 30.562 Å2
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Refinement step | Cycle: 1 / Resolution: 2.6→30.4 Å
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Refine LS restraints |
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