+Open data
-Basic information
Entry | Database: PDB / ID: 2cdv | ||||||||||||
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Title | REFINED STRUCTURE OF CYTOCHROME C3 AT 1.8 ANGSTROMS RESOLUTION | ||||||||||||
Components | CYTOCHROME C3 | ||||||||||||
Keywords | HEME PROTEIN OF ELECTRON TRANSPORT | ||||||||||||
Function / homology | Function and homology information anaerobic respiration / electron transfer activity / periplasmic space / heme binding / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Desulfovibrio vulgaris (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / Resolution: 1.8 Å | ||||||||||||
Authors | Higuchi, Y. / Kusunoki, M. / Matsuura, Y. / Yasuoka, N. / Kakudo, M. | ||||||||||||
Citation | Journal: J.Mol.Biol. / Year: 1984 Title: Refined structure of cytochrome c3 at 1.8 A resolution Authors: Higuchi, Y. / Kusunoki, M. / Matsuura, Y. / Yasuoka, N. / Kakudo, M. #1: Journal: J.Biochem.(Tokyo) / Year: 1981 Title: On Cytochrome C3 Folding Authors: Higuchi, Y. / Kusunoki, M. / Yasuoka, N. / Kakudo, M. / Yagi, T. #2: Journal: J.Biochem.(Tokyo) / Year: 1981 Title: The Structure of Cytochrome C3 from Desulfovibrio Vulgaris Miyazaki at 2.5 Angstroms Resolution Authors: Higuchi, Y. / Bando, S. / Kusunoki, M. / Matsuura, Y. / Yasuoka, N. / Kakudo, M. / Yamanaka, T. / Yagi, T. / Inokuchi, H. #3: Journal: J.Biochem.(Tokyo) / Year: 1980 Title: Amino Acid Sequence of Cytochrome C3 from Desulfovibrio Vulgaris, Miyazaki Authors: Shinkai, W. / Hase, T. / Yagi, T. / Matsubara, H. #4: Journal: J.Biochem.(Tokyo) / Year: 1979 Title: Crystallographic Data for Cytochrome C3 from Two Strains of Desulfovibrio Vulgaris, Miyazaki Authors: Bando, S. / Matsuura, Y. / Tanaka, N. / Yasuoka, N. / Kakudo, M. / Yagi, T. / Inokuchi, H. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2cdv.cif.gz | 33.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cdv.ent.gz | 26.9 KB | Display | PDB format |
PDBx/mmJSON format | 2cdv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cd/2cdv ftp://data.pdbj.org/pub/pdb/validation_reports/cd/2cdv | 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: 11557.297 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfovibrio vulgaris (bacteria) / References: UniProt: P00132 | ||
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#2: Chemical | ChemComp-HEC / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.76 % | |||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 11 ℃ / pH: 7.3 / Method: vapor diffusion | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 1.8 Å / Num. obs: 12162 / Num. measured all: 74360 / Rmerge(I) obs: 0.043 |
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-Processing
Refinement | Highest resolution: 1.8 Å /
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Refinement step | Cycle: LAST / Highest resolution: 1.8 Å
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Refinement | *PLUS Lowest resolution: 6 Å / Rfactor obs: 0.176 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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