+Open data
-Basic information
Entry | Database: PDB / ID: 6rwt | ||||||
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Title | Crystal structure of the Cbp3 homolog from Brucella abortus | ||||||
Components | Ubiquinol-cytochrome C chaperone | ||||||
Keywords | CHAPERONE / Respiratory chain / Complex III / Assembly factor / Mitochondrial translation | ||||||
Function / homology | Ubiquinol-cytochrome c chaperone, CBP3 / Ubiquinol-cytochrome c chaperone, CBP3-related / Ubiquinol-cytochrome c chaperone / Ubiquinol-cytochrome C chaperone / ACETATE ION / Ubiquinol-cytochrome C chaperone Function and homology information | ||||||
Biological species | Brucella abortus NCTC 8038 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.42 Å | ||||||
Authors | Masuyer, G. / Ndi, M. / Ott, M. / Stenmark, P. | ||||||
Funding support | Sweden, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2019 Title: Structural basis for the interaction of the chaperone Cbp3 with newly synthesized cytochromebduring mitochondrial respiratory chain assembly. Authors: Ndi, M. / Masuyer, G. / Dawitz, H. / Carlstrom, A. / Michel, M. / Elofsson, A. / Rapp, M. / Stenmark, P. / Ott, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6rwt.cif.gz | 95.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rwt.ent.gz | 76.8 KB | Display | PDB format |
PDBx/mmJSON format | 6rwt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rw/6rwt ftp://data.pdbj.org/pub/pdb/validation_reports/rw/6rwt | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 20758.957 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brucella abortus NCTC 8038 (bacteria) / Gene: BAUG_1320 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0M1WEU8 | ||||||
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#2: Chemical | #3: Chemical | #4: Chemical | #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: 2.96 Å3/Da / Density % sol: 58.43 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 20% v/v polyethylene glycol 8000, 0.1 M TRIS pH 8.0, 0.2 M magnesium chloride hexahydrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 19, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9282 Å / Relative weight: 1 |
Reflection | Resolution: 1.42→44.4 Å / Num. obs: 46643 / % possible obs: 99.9 % / Redundancy: 13.5 % / Biso Wilson estimate: 21.8 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.014 / Rrim(I) all: 0.054 / Net I/σ(I): 18 |
Reflection shell | Resolution: 1.42→1.44 Å / Redundancy: 11.5 % / Rmerge(I) obs: 1.906 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2242 / CC1/2: 0.608 / Rpim(I) all: 0.575 / Rrim(I) all: 1.992 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 1.42→44.42 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.925 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.058 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.538 Å2
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Refinement step | Cycle: LAST / Resolution: 1.42→44.42 Å
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