+Open data
-Basic information
Entry | Database: PDB / ID: 1ctj | ||||||
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Title | CRYSTAL STRUCTURE OF CYTOCHROME C6 | ||||||
Components | CYTOCHROME C6 | ||||||
Keywords | ELECTRON TRANSPORT / CYTOCHROME / HEME | ||||||
Function / homology | Function and homology information chloroplast thylakoid lumen / photosynthesis / electron transfer activity / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | Monoraphidium braunii (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.1 Å | ||||||
Authors | Sheldrick, G.M. | ||||||
Citation | Journal: Structure / Year: 1995 Title: Ab initio determination of the crystal structure of cytochrome c6 and comparison with plastocyanin. Authors: Frazao, C. / Soares, C.M. / Carrondo, M.A. / Pohl, E. / Dauter, Z. / Wilson, K.S. / Hervas, M. / Navarro, J.A. / De la Rosa, M.A. / Sheldrick, G.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ctj.cif.gz | 53.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ctj.ent.gz | 43.1 KB | Display | PDB format |
PDBx/mmJSON format | 1ctj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ctj_validation.pdf.gz | 810.2 KB | Display | wwPDB validaton report |
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Full document | 1ctj_full_validation.pdf.gz | 810.5 KB | Display | |
Data in XML | 1ctj_validation.xml.gz | 7.9 KB | Display | |
Data in CIF | 1ctj_validation.cif.gz | 10.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ct/1ctj ftp://data.pdbj.org/pub/pdb/validation_reports/ct/1ctj | HTTPS FTP |
-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 on special symmetry positions |
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-Components
#1: Protein | Mass: 9359.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Monoraphidium braunii (plant) / References: UniProt: Q09099 |
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#2: Chemical | ChemComp-HEM / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.61 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.5 | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 / Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: X11 / Wavelength: 0.80, 0.87 | |||||||||
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE AREA DETECTOR / Date: May 1, 1993 | |||||||||
Radiation | Monochromator: GE(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.1→25 Å / Num. obs: 32653 / % possible obs: 97.9 % / Observed criterion σ(I): 0 / Redundancy: 8.4 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 12.1 | |||||||||
Reflection shell | Resolution: 1.1→1.2 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.4 / % possible all: 93.5 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO / Resolution: 1.1→25 Å / Num. parameters: 8268 / Num. restraintsaints: 10326 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 0.077. CHEMICALLY EQUIVALENT BONDS AND ANGLE DISTANCES IN HEME RESTRAINED TO BE EQUAL WITHOUT TARGET VALUES. NO GEOMETRIC OR ADP ...Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 0.077. CHEMICALLY EQUIVALENT BONDS AND ANGLE DISTANCES IN HEME RESTRAINED TO BE EQUAL WITHOUT TARGET VALUES. NO GEOMETRIC OR ADP RESTRAINTS APPLIED TO IRON ATOM.
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL. V. 91 (1973) 201-228. | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 12 / Occupancy sum hydrogen: 642 / Occupancy sum non hydrogen: 822.83 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→25 Å
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Refine LS restraints |
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