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Yorodumi- PDB-3c63: Tetrameric Cytochrome cb562 (K34/H59/D62/H63/H73/A74/H77) Assembl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3c63 | ||||||
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Title | Tetrameric Cytochrome cb562 (K34/H59/D62/H63/H73/A74/H77) Assembly Stabilized by Interprotein Zinc Coordination | ||||||
Components | Soluble cytochrome b562 | ||||||
Keywords | ELECTRON TRANSPORT / 16-helix bundle / interfacial Zn-coordination / Heme / Iron / Metal-binding / Transport | ||||||
Function / homology | Function and homology information electron transport chain / periplasmic space / electron transfer activity / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.75 Å | ||||||
Authors | Tezcan, F.A. / Salgado, E.N. / Lewis, R.A. / Faraone-Mennella, J. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2008 Title: Metal-mediated self-assembly of protein superstructures: influence of secondary interactions on protein oligomerization and aggregation. Authors: Salgado, E.N. / Lewis, R.A. / Faraone-Mennella, J. / 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 | 3c63.cif.gz | 111.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3c63.ent.gz | 85.1 KB | Display | PDB format |
PDBx/mmJSON format | 3c63.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3c63_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 3c63_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 3c63_validation.xml.gz | 25.9 KB | Display | |
Data in CIF | 3c63_validation.cif.gz | 36.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c6/3c63 ftp://data.pdbj.org/pub/pdb/validation_reports/c6/3c63 | HTTPS FTP |
-Related structure data
Related structure data | 3c62C 2bc5S S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 11612.022 Da / Num. of mol.: 4 / Mutation: R34K, K59H, R62D, D73H, D74A, 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-ZN / #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: 2.16 Å3/Da / Density % sol: 43.14 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 12% PEG 400, 200 mM CaCl2, 100 mM TRIS, 1.25 mM ZnCl2, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 Å |
Detector | Type: APEX II CCD / Detector: CCD / Date: Jan 30, 2008 / Details: microcapillary collimator |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. all: 39850 / Num. obs: 37193 / % possible obs: 93.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.76 % / Biso Wilson estimate: 12.2 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 1.75→1.78 Å / Redundancy: 1.14 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.98 / Num. unique all: 652 / Rsym value: 0.51 / % possible all: 82.1 |
-Processing
Software |
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Refinement | Starting model: PDB entry 2BC5 Resolution: 1.75→20.24 Å / FOM work R set: 0.855 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Used weighted full matrix least squares procedure
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Solvent computation | Bsol: 47.124 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.487 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→20.24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.76 Å /
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Xplor file |
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