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Yorodumi- PDB-3m79: A tetrameric Zn-bound cytochrome cb562 complex with covalently an... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3m79 | ||||||
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Title | A tetrameric Zn-bound cytochrome cb562 complex with covalently and non-covalently stabilized interfaces crystallized in the presence of Cu(II) and Zn(II) | ||||||
Components | Soluble cytochrome b562 | ||||||
Keywords | OXIDOREDUCTASE / Tetramer of Four Helix Bundles / Electron transport / Heme / Iron / Metal-binding / 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: 2.1 Å | ||||||
Authors | Brodin, J.D. / Tezcan, F.A. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2010 Title: Evolution of metal selectivity in templated protein interfaces. Authors: Brodin, J.D. / Medina-Morales, A. / Ni, T. / Salgado, E.N. / Ambroggio, X.I. / 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 | 3m79.cif.gz | 191.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3m79.ent.gz | 155.3 KB | Display | PDB format |
PDBx/mmJSON format | 3m79.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m7/3m79 ftp://data.pdbj.org/pub/pdb/validation_reports/m7/3m79 | HTTPS FTP |
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-Related structure data
Related structure data | 3iq5C 3iq6SC 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 3 / Auth seq-ID: 1 - 106 / Label seq-ID: 1 - 106
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Details | Tetramer |
-Components
#1: Protein | Mass: 11701.123 Da / Num. of mol.: 8 Mutation: R34A, L38A, Q41W, K42S, K59H, D66W, V69I, D73H, K77H, T96C, 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-HEM / #3: Chemical | ChemComp-ZN / #4: 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: 2.36 Å3/Da / Density % sol: 47.94 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 16, 2010 Details: Vertical focusing mirror; single crystal (Si111) bent monochromator (horizontal focusing) |
Radiation | Monochromator: side scattering I-beam bent single crystal; asymmetric cut 4.9650 deg. Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.099→89.17 Å / Num. all: 49272 / Num. obs: 49272 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.5 % / Rsym value: 0.102 / Net I/σ(I): 4 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 10.3 % / Mean I/σ(I) obs: 1.5 / Num. unique all: 6358 / Rsym value: 0.176 / % possible all: 84.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3IQ6 Resolution: 2.1→59.87 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.891 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.812 / SU B: 9.153 / SU ML: 0.156 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.325 / ESU R Free: 0.239 / 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 max: 92.21 Å2 / Biso mean: 27.461 Å2 / Biso min: 9.68 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→59.87 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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