[English] 日本語
Yorodumi- PDB-5cp0: MAS complex structure of peptide deformylase from Xanthomonas ory... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5cp0 | ||||||
---|---|---|---|---|---|---|---|
Title | MAS complex structure of peptide deformylase from Xanthomonas oryzae pv oryzae | ||||||
Components |
| ||||||
Keywords | HYDROLASE/SUBSTRATE / substrate / HYDROLASE-SUBSTRATE 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) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Ngo, H.P.T. / Kang, L.W. | ||||||
Citation | Journal: To Be Published Title: MAS complex structure of peptide deformylase from Xanthomonas oryzae pv oryzae Authors: Ngo, H.P.T. / Kang, L.W. #1: Journal: To Be Published Title: Substrates complexed structure of XOO1075, a peptide defromylase from xanthomonas oryzae pv. oryzae Authors: Ngo, H.P.T. / Kang, L.W. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5cp0.cif.gz | 55.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5cp0.ent.gz | 38 KB | Display | PDB format |
PDBx/mmJSON format | 5cp0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5cp0_validation.pdf.gz | 448.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5cp0_full_validation.pdf.gz | 453 KB | Display | |
Data in XML | 5cp0_validation.xml.gz | 11.8 KB | Display | |
Data in CIF | 5cp0_validation.cif.gz | 16.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cp/5cp0 ftp://data.pdbj.org/pub/pdb/validation_reports/cp/5cp0 | HTTPS FTP |
-Related structure data
Related structure data | 3dld S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
-Protein / Protein/peptide , 2 types, 2 molecules AC
#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 / Plasmid: pet11a / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: Q5H3Z2, peptide deformylase |
---|---|
#2: Protein/peptide | Mass: 307.367 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 4 types, 202 molecules
#3: Chemical | ChemComp-CD / #4: Chemical | #5: Chemical | ChemComp-NA / | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.4 Å3/Da / Density % sol: 63.82 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.99 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 20, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. obs: 20724 / % possible obs: 98.6 % / Redundancy: 9.9 % / Net I/σ(I): 36.2 |
Reflection shell | Resolution: 1.95→1.98 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.652 / Mean I/σ(I) obs: 4.6 / % possible all: 95.7 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3DLD 3dld Resolution: 2→29.37 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.042 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 28.556 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→29.37 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|