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Yorodumi- PDB-4eif: Crystal structure of cytochrome c6C L50Q mutant from Synechococcu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4eif | |||||||||
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Title | Crystal structure of cytochrome c6C L50Q mutant from Synechococcus sp. PCC 7002 | |||||||||
Components | Cytochrome c6 | |||||||||
Keywords | ELECTRON TRANSPORT / cytochrome c6C | |||||||||
Function / homology | Function and homology information plasma membrane-derived thylakoid lumen / photosynthesis / electron transfer activity / iron ion binding / heme binding Similarity search - Function | |||||||||
Biological species | Synechococcus sp. (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.04 Å | |||||||||
Authors | Krzywda, S. / Bialek, W. / Zatwarnicki, P. / Jaskolski, M. / Szczepaniak, A. | |||||||||
Citation | Journal: To be Published Title: Cytochrome c6 and c6C from Synechococcus sp. PCC 7002 - structure and function. Authors: Bialek, W. / Krzywda, S. / Zatwarnicki, P. / Jaskolski, M. / Szczepaniak, A. #1: Journal: Biochemistry / Year: 2008 Title: Deeply branching c6-like cytochromes of cyanobacteria. Authors: Bialek, W. / Nelson, M. / Tamiola, K. / Kallas, T. / Szczepaniak, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4eif.cif.gz | 58.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4eif.ent.gz | 41.1 KB | Display | PDB format |
PDBx/mmJSON format | 4eif.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ei/4eif ftp://data.pdbj.org/pub/pdb/validation_reports/ei/4eif | HTTPS FTP |
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-Related structure data
Related structure data | 4eicC 4eidC 4eieSC 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: 9427.482 Da / Num. of mol.: 1 / Fragment: UNP Residues 29-115 / Mutation: L50Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechococcus sp. (bacteria) / Strain: ATCC 27264 / PCC 7002 / PR-6 / Description: co-expression with pEC86 / Gene: petJ, petJ2, SYNPCC7002_A2391 / Plasmid: pUCPF2 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5a / References: UniProt: Q8KX15 | ||||
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#2: Chemical | ChemComp-HEC / | ||||
#3: Chemical | #4: Chemical | ChemComp-CL / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.69 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Protein solution: 15 mg/ml cytochrome c6C in 0.1 M TRIS pH 7.5, 0.2 M NaCl and 1 mM PMSF; Precipitant solution: 2 M NaCl and 2 M NH4)2SO4., VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8123 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Dec 5, 2011 / Details: mirrors |
Radiation | Monochromator: Triangular Si (111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8123 Å / Relative weight: 1 |
Reflection | Resolution: 1.04→31.18 Å / Num. all: 39071 / Num. obs: 39071 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.4 % / Biso Wilson estimate: 10.127 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 22.25 |
Reflection shell | Resolution: 1.04→1.1 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.244 / Mean I/σ(I) obs: 7.8 / Num. measured obs: 44534 / Num. unique all: 5898 / Num. unique obs: 5898 / % possible all: 98.7 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4EIE Resolution: 1.04→31.18 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.971 / WRfactor Rfree: 0.133 / WRfactor Rwork: 0.109 / Occupancy max: 1 / Occupancy min: 0 / SU B: 0.518 / SU ML: 0.013 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.021 / ESU R Free: 0.023 / Stereochemistry target values: Engh & Huber / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 44.28 Å2 / Biso mean: 10.5564 Å2 / Biso min: 3.75 Å2
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Refinement step | Cycle: LAST / Resolution: 1.04→31.18 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 / % reflection obs: 100 %
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