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Yorodumi- PDB-3de8: Crystal Structure of a Dimeric Cytochrome cb562 Assembly Induced ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3de8 | ||||||
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Title | Crystal Structure of a Dimeric Cytochrome cb562 Assembly Induced by Copper Coordination | ||||||
Components | Soluble cytochrome b562 | ||||||
Keywords | METAL BINDING PROTEIN / Cu-stabilized dimeric superstructure / Electron transport / Heme / Iron / Metal-binding / Periplasm / Transport | ||||||
Function / homology | Function and homology information electron transfer activity / periplasmic space / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å | ||||||
Authors | Salgado, E.N. / Lewis, R.A. / Rheingold, A.L. / Tezcan, F.A. | ||||||
Citation | Journal: Inorg.Chem. / Year: 2009 Title: Control of protein oligomerization symmetry by metal coordination: C2 and C3 symmetrical assemblies through Cu(II) and Ni(II) coordination. Authors: Salgado, E.N. / Lewis, R.A. / Mossin, S. / Rheingold, A.L. / Tezcan, F.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3de8.cif.gz | 111.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3de8.ent.gz | 85.7 KB | Display | PDB format |
PDBx/mmJSON format | 3de8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/de/3de8 ftp://data.pdbj.org/pub/pdb/validation_reports/de/3de8 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 11726.153 Da / Num. of mol.: 4 / Mutation: K59H, D73H, K77H, R98C, Y101C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cybC / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABE7 #2: Chemical | ChemComp-CU / #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-HEM / #5: 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: 2.2 Å3/Da / Density % sol: 44.19 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 100 mM Hepes, 25% PEG 3350, 200 mM CaCl2, 17.8 mM CuSO4, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.008 Å |
Detector | Type: ADSC Quantum 325 / Detector: CCD / Date: Mar 23, 2008 |
Radiation | Monochromator: Flat collimating mirror, double crystal monochromator, toroid focusing mirror Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.008 Å / Relative weight: 1 |
Reflection | Resolution: 1.72→50 Å / Num. obs: 42391 / % possible obs: 98.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.7 % / Rsym value: 0.075 |
Reflection shell | Resolution: 1.72→1.78 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 8.7 / Rsym value: 0.209 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.72→32.92 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.919 / SU B: 4.316 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.142 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 mean: 24.014 Å2
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Refinement step | Cycle: LAST / Resolution: 1.72→32.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.72→1.765 Å / Total num. of bins used: 20
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