+Open data
-Basic information
Entry | Database: PDB / ID: 2ce0 | ||||||
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Title | Structure of oxidized Arabidopsis thaliana cytochrome 6A | ||||||
Components | CYTOCHROME C6 | ||||||
Keywords | ELECTRON TRANSFER / CHLOROPLAST / ELECTRON TRANSPORT / HEME / IRON / THYLAKOID / PHOTOSYNTHESIS / METAL-BINDING | ||||||
Function / homology | Function and homology information chloroplast thylakoid lumen / photosynthesis / electron transfer activity / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | ARABIDOPSIS THALIANA (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 Å | ||||||
Authors | Marcaida, M.J. / Schlarb-Ridley, B.G. / Worrall, J.A.R. / Wastl, J. / Evans, T.J. / Bendall, D.S. / Luisi, B.F. / Howe, C.J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: Structure of Cytochrome C(6A), a Novel Dithio-Cytochrome of Arabidopsis Thaliana, and its Reactivity with Plastocyanin: Implications for Function. Authors: Marcaida, M.J. / Schlarb-Ridley, B.G. / Worrall, J.A.R. / Wastl, J. / Evans, T.J. / Bendall, D.S. / Luisi, B.F. / Howe, C.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ce0.cif.gz | 62.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ce0.ent.gz | 45.8 KB | Display | PDB format |
PDBx/mmJSON format | 2ce0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ce/2ce0 ftp://data.pdbj.org/pub/pdb/validation_reports/ce/2ce0 | HTTPS FTP |
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-Related structure data
Related structure data | 2ce1C 1ctjS C: citing same article (ref.) 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 11688.068 Da / Num. of mol.: 1 / Fragment: CYTOCHROME C6, RESIDUES 71-175 / Mutation: YES Source method: isolated from a genetically manipulated source Details: HEME GROUP AND DISULPHIDE BOND BETWEEN C67 AND C73 / Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Plasmid: PBATC6A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): GM119 / References: UniProt: Q93VA3 |
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#2: Chemical | ChemComp-HEC / |
#3: Water | ChemComp-HOH / |
Compound details | ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.09 % |
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Crystal grow | Details: 1.26 M AMMONIUM SULFATE, 100 MM ACETATE PH 4.5 AND 200 MM NACL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9795 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→30 Å / Num. obs: 40175 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 11.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 24.8 |
Reflection shell | Resolution: 1.2→1.24 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 4.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1CTJ Resolution: 1.24→7.99 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.181 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.046 / ESU R Free: 0.046 Stereochemistry target values: MAXIMUM LIKELIHOODWITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.9 Å2
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Refinement step | Cycle: LAST / Resolution: 1.24→7.99 Å
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Refine LS restraints |
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