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Yorodumi- PDB-1qle: CRYO-STRUCTURE OF THE PARACOCCUS DENITRIFICANS FOUR-SUBUNIT CYTOC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qle | |||||||||
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Title | CRYO-STRUCTURE OF THE PARACOCCUS DENITRIFICANS FOUR-SUBUNIT CYTOCHROME C OXIDASE IN THE COMPLETELY OXIDIZED STATE COMPLEXED WITH AN ANTIBODY FV FRAGMENT | |||||||||
Components |
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Keywords | OXIDOREDUCTASE/IMMUNE SYSTEM / COMPLEX (OXIDOREDUCTASE-ANTIBODY) / ELECTRON TRANSPORT / TRANSMEMBRANE / CYTOCHROME OXIDASE / ANTIBODY COMPLEX / OXIDOREDUCTASE-IMMUNE SYSTEM complex | |||||||||
Function / homology | Function and homology information aerobic electron transport chain / respiratory chain complex IV / cytochrome-c oxidase / oxidative phosphorylation / cytochrome-c oxidase activity / electron transport coupled proton transport / : / ATP synthesis coupled electron transport / copper ion binding / heme binding ...aerobic electron transport chain / respiratory chain complex IV / cytochrome-c oxidase / oxidative phosphorylation / cytochrome-c oxidase activity / electron transport coupled proton transport / : / ATP synthesis coupled electron transport / copper ion binding / heme binding / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | MUS MUSCULUS (house mouse) PARACOCCUS DENITRIFICANS (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 3 Å | |||||||||
Authors | Harrenga, A. / Michel, H. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 1999 Title: The Cytochrome C Oxidase from Paracoccus Denitrificans Does not Change the Metal Center Ligation Upon Reduction Authors: Harrenga, A. / Michel, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qle.cif.gz | 275.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qle.ent.gz | 227.7 KB | Display | PDB format |
PDBx/mmJSON format | 1qle.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qle_validation.pdf.gz | 660.1 KB | Display | wwPDB validaton report |
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Full document | 1qle_full_validation.pdf.gz | 739.3 KB | Display | |
Data in XML | 1qle_validation.xml.gz | 38.6 KB | Display | |
Data in CIF | 1qle_validation.cif.gz | 56.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ql/1qle ftp://data.pdbj.org/pub/pdb/validation_reports/ql/1qle | HTTPS FTP |
-Related structure data
Related structure data | |
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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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Details | THE CRYSTAL STRUCTURE SHOWS A CRYSTAL PACKING ARRANGEMENT WHERETHERE IS CONTACT BETWEEN CHAINS C AND H GIVING A CYCLICPACKING WITHCHAIN- H ... (CHAIN-C...CHAIN-H) ... CHAIN-C(Y,-X,Z ) ASU: X,Y,Z (-Y,X,Z) |
-Components
-CYTOCHROME C OXIDASE POLYPEPTIDE ... , 3 types, 3 molecules ABC
#1: Protein | Mass: 60354.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) PARACOCCUS DENITRIFICANS (bacteria) / Cellular location: CYTOPLASMIC MEMBRANE / References: UniProt: P98002, cytochrome-c oxidase |
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#2: Protein | Mass: 27972.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) PARACOCCUS DENITRIFICANS (bacteria) / Cellular location: CYTOPLASMIC MEMBRANE / References: UniProt: P08306, cytochrome-c oxidase |
#3: Protein | Mass: 30676.975 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) PARACOCCUS DENITRIFICANS (bacteria) / Cellular location: CYTOPLASMIC MEMBRANE / References: UniProt: P06030, cytochrome-c oxidase |
-Protein/peptide , 1 types, 1 molecules D
#4: Protein/peptide | Mass: 4701.407 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) PARACOCCUS DENITRIFICANS (bacteria) / Cellular location: CYTOPLASMIC MEMBRANE / References: UniProt: P77921, cytochrome-c oxidase |
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-Antibody , 2 types, 2 molecules HL
#5: Antibody | Mass: 13356.854 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) |
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#6: Antibody | Mass: 11786.118 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) |
-Non-polymers , 6 types, 8 molecules
#7: Chemical | #8: Chemical | ChemComp-CU / | #9: Chemical | ChemComp-CA / | #10: Chemical | ChemComp-MN / | #11: Chemical | ChemComp-CUA / | #12: Chemical | |
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-Details
Sequence details | THE SEQUENCE OF VH AND VL IS DESCRIBED IN THE FOLLOWING REFERENCE, OSTERMEIER C. ET AL. (1995) ...THE SEQUENCE OF VH AND VL IS DESCRIBED IN THE FOLLOWING REFERENCE, OSTERMEIER |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 5.74 Å3/Da / Density % sol: 75 % | ||||||||||||||||||||||||
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Crystal grow | pH: 8 / Details: pH 8.00 | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 14 ℃ / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID2 / Wavelength: 0.9875 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9875 Å / Relative weight: 1 |
Reflection | Resolution: 3→20 Å / Num. obs: 64653 / % possible obs: 95.2 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 32.2 Å2 / Rmerge(I) obs: 0.115 / Net I/σ(I): 9.6 |
Reflection | *PLUS Num. measured all: 165650 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 3→6 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 5840810 / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 31.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.16 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
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Software | *PLUS Name: CNS / Version: 0.3 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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