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Yorodumi- PDB-3hb3: High resolution crystal structure of Paracoccus denitrificans cyt... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hb3 | ||||||
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Title | High resolution crystal structure of Paracoccus denitrificans cytochrome c oxidase | ||||||
Components |
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Keywords | OXIDOREDUCTASE / Electron transfer / Proton transfer / Proton pumping / Membrane protein / Cell inner membrane / Cell membrane / Copper / Disulfide bond / Electron transport / Heme / Hydrogen ion transport / Ion transport / Iron / Membrane / Metal-binding / Respiratory chain / Transmembrane / Transport / Pyrrolidone carboxylic acid | ||||||
Function / homology | Function and homology information respiratory chain complex IV / cytochrome-c oxidase / oxidative phosphorylation / immunoglobulin complex / cytochrome-c oxidase activity / immunoglobulin mediated immune response / electron transport coupled proton transport / : / ATP synthesis coupled electron transport / antigen binding ...respiratory chain complex IV / cytochrome-c oxidase / oxidative phosphorylation / immunoglobulin complex / cytochrome-c oxidase activity / immunoglobulin mediated immune response / electron transport coupled proton transport / : / ATP synthesis coupled electron transport / antigen binding / adaptive immune response / immune response / copper ion binding / heme binding / extracellular space / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Paracoccus denitrificans (bacteria) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Koepke, J. / Angerer, H. / Peng, G. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2009 Title: High resolution crystal structure of Paracoccus denitrificans cytochrome c oxidase: New insights into the active site and the proton transfer pathways Authors: Koepke, J. / Olkhova, E. / Angerer, H. / Muller, H. / Peng, G. / Michel, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hb3.cif.gz | 255.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hb3.ent.gz | 202.3 KB | Display | PDB format |
PDBx/mmJSON format | 3hb3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3hb3_validation.pdf.gz | 4.5 MB | Display | wwPDB validaton report |
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Full document | 3hb3_full_validation.pdf.gz | 4.6 MB | Display | |
Data in XML | 3hb3_validation.xml.gz | 63.3 KB | Display | |
Data in CIF | 3hb3_validation.cif.gz | 86.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hb/3hb3 ftp://data.pdbj.org/pub/pdb/validation_reports/hb/3hb3 | HTTPS FTP |
-Related structure data
Related structure data | 1ar1S 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
-Cytochrome c oxidase subunit ... , 2 types, 2 molecules AB
#1: Protein | Mass: 62486.645 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Gene: ctaDII / Production host: Escherichia coli (E. coli) / References: UniProt: P98002, cytochrome-c oxidase |
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#2: Protein | Mass: 32563.643 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Gene: ctaC, coiI, ctaB / Production host: Escherichia coli (E. coli) / References: UniProt: P08306, cytochrome-c oxidase |
-Antibody , 2 types, 2 molecules CD
#3: Antibody | Mass: 14324.923 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P18525*PLUS |
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#4: Antibody | Mass: 13260.795 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P01636*PLUS |
-Sugars , 1 types, 14 molecules
#10: Sugar | ChemComp-LMT / |
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-Non-polymers , 7 types, 572 molecules
#5: Chemical | #6: Chemical | #7: Chemical | ChemComp-MN / | #8: Chemical | ChemComp-CA / | #9: Chemical | ChemComp-LDA / #11: Chemical | ChemComp-PEO / | #12: Water | ChemComp-HOH / | |
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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: 4.02 Å3/Da / Density % sol: 69.41 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 5.5 Details: 25% glycerol, pH 5.5, VAPOR DIFFUSION, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9198 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 4, 2005 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9198 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→111.8 Å / Num. all: 90709 / Num. obs: 90709 / % possible obs: 99.04 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 2.25→2.32 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 3.2 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1AR1 Resolution: 2.25→19.98 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.89 / SU B: 7.585 / SU ML: 0.176 / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R: 0.209 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.272 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→19.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.308 Å / Total num. of bins used: 20
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