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Yorodumi- PDB-3kh7: Crystal structure of the periplasmic soluble domain of reduced Cc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kh7 | ||||||
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Title | Crystal structure of the periplasmic soluble domain of reduced CcmG from Pseudomonas aeruginosa | ||||||
Components | Thiol:disulfide interchange protein dsbE | ||||||
Keywords | OXIDOREDUCTASE / TRX-like / thiol-disulfide exchange / Cell inner membrane / Cytochrome c-type biogenesis / Disulfide bond / Redox-active center / Transmembrane | ||||||
Function / homology | Function and homology information cytochrome complex assembly / disulfide oxidoreductase activity / outer membrane-bounded periplasmic space / plasma membrane Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Di Matteo, A. / Calosci, N. / Gianni, S. / Jemth, P. / Brunori, M. / Travaglini Allocatelli, C. | ||||||
Citation | Journal: Proteins / Year: 2010 Title: Structural and functional characterization of CcmG from Pseudomonas aeruginosa, a key component of the bacterial cytochrome c maturation apparatus. Authors: Di Matteo, A. / Calosci, N. / Gianni, S. / Jemth, P. / Brunori, M. / Travaglini-Allocatelli, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kh7.cif.gz | 48.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kh7.ent.gz | 32.5 KB | Display | PDB format |
PDBx/mmJSON format | 3kh7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3kh7_validation.pdf.gz | 421.7 KB | Display | wwPDB validaton report |
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Full document | 3kh7_full_validation.pdf.gz | 421.7 KB | Display | |
Data in XML | 3kh7_validation.xml.gz | 9.3 KB | Display | |
Data in CIF | 3kh7_validation.cif.gz | 12.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kh/3kh7 ftp://data.pdbj.org/pub/pdb/validation_reports/kh/3kh7 | HTTPS FTP |
-Related structure data
Related structure data | 3kh9C 1kngS C: citing same article (ref.) 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
#1: Protein | Mass: 19560.182 Da / Num. of mol.: 1 / Fragment: Soluble domain residues 26-180 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: ccmG, dsbE, PA1481 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I3N1 |
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#2: 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: 2.36 Å3/Da / Density % sol: 47.83 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 18-20% PEG 4000 W/V, 0.1-0.3 M magnesium formate, 0.1M sodium citrate pH 5.6, 5% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.933 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 21, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. all: 19403 / Num. obs: 19387 / % possible obs: 99.9 % / Redundancy: 14.3 % / Rmerge(I) obs: 0.09 / Χ2: 0.998 / Net I/σ(I): 12 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 13.1 % / Rmerge(I) obs: 0.394 / Num. unique all: 1891 / Χ2: 0.844 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1KNG Resolution: 1.75→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.949 / Occupancy max: 1 / Occupancy min: 0 / SU B: 2.313 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 49.72 Å2 / Biso mean: 21.816 Å2 / Biso min: 8.03 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.847 Å / Total num. of bins used: 20
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