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Yorodumi- PDB-1jaf: CRYSTAL STRUCTURE OF CYTOCHROME C' FROM RHODOCYCLUS GELATINOSUS A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jaf | ||||||
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Title | CRYSTAL STRUCTURE OF CYTOCHROME C' FROM RHODOCYCLUS GELATINOSUS AT 2.5 ANGSTOMS RESOLUTION | ||||||
Components | CYTOCHROME C' | ||||||
Keywords | ELECTRON TRANSPORT / HEME PROTEIN / CYTOCHROME C' | ||||||
Function / homology | Function and homology information electron transport chain / periplasmic space / electron transfer activity / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | Rubrivivax gelatinosus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Archer, M. / Banci, L. / Dikaya, E. / Romao, M.J. | ||||||
Citation | Journal: J.Biol.Inorg.Chem. / Year: 1997 Title: Crystal Structure of Cytochrome C' from Rhodocyclus Gelatinosus and Comparison with Other Cytochromes C' Authors: Archer, M. / Banci, L. / Dikaya, E. / Romao, M.J. #1: Journal: Biochemistry / Year: 1993 Title: One-and Two-Dimensional NMR Characterization of Oxidized and Reduced Cytochrome C' from Rhodocyclus Gelatinosus Authors: Bertini, I. / Gori, G. / Luchinat, C. / Vila, A.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jaf.cif.gz | 55.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jaf.ent.gz | 44.3 KB | Display | PDB format |
PDBx/mmJSON format | 1jaf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jaf_validation.pdf.gz | 537.8 KB | Display | wwPDB validaton report |
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Full document | 1jaf_full_validation.pdf.gz | 542 KB | Display | |
Data in XML | 1jaf_validation.xml.gz | 6.9 KB | Display | |
Data in CIF | 1jaf_validation.cif.gz | 10.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ja/1jaf ftp://data.pdbj.org/pub/pdb/validation_reports/ja/1jaf | HTTPS FTP |
-Related structure data
Related structure data | 1cgoS 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
#1: Protein | Mass: 13303.056 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rubrivivax gelatinosus (bacteria) / References: UniProt: P00142 #2: Chemical | #3: 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: 3.5 Å3/Da / Density % sol: 60 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6 Details: 55% SATURATED (NH4)2SO4, 50 MM (NH4)2HPO4, 1 M NACL, pH 6. | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 277 K / Method: batch method | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Type: BRUKER NONIUS / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→27.4 Å / Num. obs: 13010 / % possible obs: 99.3 % / Redundancy: 7.4 % / Biso Wilson estimate: 47.7 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 2.5→2.59 Å / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 2.4 / % possible all: 98.7 |
Reflection | *PLUS Num. measured all: 96234 / Rmerge(I) obs: 0.112 |
Reflection shell | *PLUS % possible obs: 98.7 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: CYTOCHROME C' FROM ALCALIGENES SP (PDB ENTRY 1CGO) Resolution: 2.5→27.4 Å / Cross valid method: FREE R / σ(F): 2 Details: BULK SOLVENT CORRECTION USED (KSOL=0.33, SOLRAD=0.25 A, B=50 A**2).
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Displacement parameters | Biso mean: 34.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→27.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.59 Å
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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