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Yorodumi- PDB-2yiu: X-ray structure of the dimeric cytochrome BC1 complex from the so... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yiu | ||||||
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Title | X-ray structure of the dimeric cytochrome BC1 complex from the soil bacterium paracoccus denitrificans at 2.7 angstrom resolution | ||||||
Components |
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Keywords | OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information respiratory chain complex III / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / : / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / membrane => GO:0016020 / electron transfer activity / heme binding / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | PARACOCCUS DENITRIFICANS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Kleinschroth, T. / Castellani, M. / Trinh, C.H. / Morgner, N. / Brutschy, B. / Ludwig, B. / Hunte, C. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2011 Title: X-Ray Structure of the Dimeric Cytochrome Bc(1) Complex from the Soil Bacterium Paracoccus Denitrificans at 2.7-A Resolution. Authors: Kleinschroth, T. / Castellani, M. / Trinh, C.H. / Morgner, N. / Brutschy, B. / Ludwig, B. / Hunte, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yiu.cif.gz | 335.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yiu.ent.gz | 266.4 KB | Display | PDB format |
PDBx/mmJSON format | 2yiu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2yiu_validation.pdf.gz | 2.9 MB | Display | wwPDB validaton report |
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Full document | 2yiu_full_validation.pdf.gz | 3 MB | Display | |
Data in XML | 2yiu_validation.xml.gz | 68.1 KB | Display | |
Data in CIF | 2yiu_validation.cif.gz | 89.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yi/2yiu ftp://data.pdbj.org/pub/pdb/validation_reports/yi/2yiu | HTTPS FTP |
-Related structure data
Related structure data | 2qjyS 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
-Protein , 3 types, 6 molecules ADBECF
#1: Protein | Mass: 51536.176 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: C-TERMINAL DECA-HIS TAG / Source: (natural) PARACOCCUS DENITRIFICANS (bacteria) / Variant: MK6 PMC1 (FBC-OPERON) / Strain: PD1222 / References: UniProt: P05418, quinol-cytochrome-c reductase #2: Protein | Mass: 28491.744 Da / Num. of mol.: 2 / Fragment: RESIDUES 25-450 / Source method: isolated from a natural source Details: DELETION OF AMINO ACIDS 39 TO 201 COMPARED TO WILD-TYPE Source: (natural) PARACOCCUS DENITRIFICANS (bacteria) / Variant: MK6 PMC1 (FBC-OPERON) / Strain: PD1222 / References: UniProt: P13627, quinol-cytochrome-c reductase #3: Protein | Mass: 20321.539 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) PARACOCCUS DENITRIFICANS (bacteria) / Variant: MK6 PMC1 (FBC-OPERON) / Strain: PD1222 / References: UniProt: P05417, quinol-cytochrome-c reductase |
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-Non-polymers , 5 types, 16 molecules
#4: Chemical | ChemComp-HEM / #5: Chemical | #6: Chemical | #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | PROTOPORPHSequence details | NO C-TERMINAL DECA-HIS TAG IN THE DATABANK SEQUENCE. AMINO ACIDS 39-201(CHAINS B AND E) WERE ...NO C-TERMINAL DECA-HIS TAG IN THE DATABANK SEQUENCE. AMINO ACIDS 39-201(CHAINS B AND E) WERE DELETED IN THE MUTANT COMPARED TO THE WILD-TYPE SEQUENCE IN THE DATABASE. THE SEQUENCE BELOW IS THE ONE OF THE DELETION VARIANT. CHAIN, B, E. NUMBERING OF SUBUNIT CYT C1DELTAAC INCLUDES THE PREDICTED SIGNAL SEQUENCE (RESIDUES 1-24), BUT LACKS THE SEQUENCE FOR THE ACIDIC DOMAIN OF WILD-TYPE CYT C1 (RESIDUES 39-201 OF WILD-TYPE CYT C1). | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.59 Å3/Da / Density % sol: 66 % / Description: NONE |
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Crystal grow | pH: 4.6 Details: 100 MM SODIUM ACETATE, PH 4.6, 50 MM NACL, 30% 2-METHYL 2,4-PENTANDIOL (MPD) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Aug 8, 2009 / Details: KIRKPATRICK-BAEZ MIRROR PAIR |
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR TWO SI III CRYSTALS Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→54.97 Å / Num. obs: 70055 / % possible obs: 95 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 40.7 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 3.7 |
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.2 / % possible all: 90 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2QJY Resolution: 2.7→97.96 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.886 / SU B: 11.368 / SU ML: 0.241 / Cross valid method: THROUGHOUT / ESU R: 0.629 / ESU R Free: 0.36 / 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 mean: 28.805 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→97.96 Å
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Refine LS restraints |
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