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Yorodumi- PDB-1c53: S-CLASS CYTOCHROMES C HAVE A VARIETY OF FOLDING PATTERNS: STRUCTU... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1c53 | ||||||
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Title | S-CLASS CYTOCHROMES C HAVE A VARIETY OF FOLDING PATTERNS: STRUCTURE OF CYTOCHROME C-553 FROM DESULFOVIBRIO VULGARIS DETERMINED BY THE MULTI-WAVELENGTH ANOMALOUS DISPERSION METHOD | ||||||
Components | CYTOCHROME C553 | ||||||
Keywords | ELECTRON TRANSPORT | ||||||
Function / homology | Function and homology information electron transfer activity / periplasmic space / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | Desulfovibrio vulgaris str. 'Miyazaki F' (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.8 Å | ||||||
Authors | Nakagawa, A. / Higuchi, Y. / Yasuoka, N. / Katsube, Y. / Yaga, T. | ||||||
Citation | Journal: J.Biochem.(Tokyo) / Year: 1990 Title: S-class cytochromes c have a variety of folding patterns: structure of cytochrome c-553 from Desulfovibrio vulgaris determined by the multi-wavelength anomalous dispersion method. Authors: Nakagawa, A. / Higuchi, Y. / Yasuoka, N. / Katsube, Y. / Yagi, T. #1: Journal: Acta Crystallogr.,Sect.A / Year: 1990 Title: Structure Determination of Cytochrome C-553 from Desulfovibrio Vulgaris Miyazaki F Determined by the Multi-Wavelength Anomalous Dispersion Method Authors: Nakagawa, A. / Higuchi, Y. / Yasuoka, N. / Katsube, Y. / Yagi, T. #2: Journal: J.Biochem.(Tokyo) / Year: 1986 Title: Crystallographic Study of Cytochrome C553 from Desulfovibrio Vulgaris Miyazaki Authors: Nakagawa, A. / Nagashima, E. / Higuchi, Y. / Kusunoki, M. / Matsuura, Y. / Yasuoka, N. / Katsube, Y. / Chihara, H. / Yagi, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1c53.cif.gz | 13.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1c53.ent.gz | 6.5 KB | Display | PDB format |
PDBx/mmJSON format | 1c53.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c5/1c53 ftp://data.pdbj.org/pub/pdb/validation_reports/c5/1c53 | 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: 8411.668 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfovibrio vulgaris str. 'Miyazaki F' (bacteria) Species: Desulfovibrio vulgaris / Strain: Miyazaki / References: UniProt: P00120 |
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#2: Chemical | ChemComp-HEM / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.1 % | ||||||||||||||||||||
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Crystal grow | *PLUS Method: microdialysisDetails: referred to 'Nakagawa, A.', (1986) J.Biochem.(Tokyo), 99, 605-606 | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Processing
Software | Name: PROLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.8→10 Å / σ(F): 1 /
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Refinement step | Cycle: LAST / Resolution: 1.8→10 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 10 Å / Num. reflection obs: 8855 / σ(F): 1 / Rfactor obs: 0.194 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: p_angle_d / Dev ideal: 0.35 |