[English] 日本語
Yorodumi- PDB-3iq5: Crystal structure of an engineered metal-free tetrameric cytochro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3iq5 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of an engineered metal-free tetrameric cytochrome cb562 complex templated by Zn-coordination | ||||||
Components | Soluble cytochrome b562 | ||||||
Keywords | ELECTRON TRANSPORT / Tetramer of Four-Helix Bundles with Interfacial Disulfide Bonds / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å | ||||||
Authors | Brodin, J.N. / 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3iq5.cif.gz | 103.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3iq5.ent.gz | 80.4 KB | Display | PDB format |
PDBx/mmJSON format | 3iq5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3iq5_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3iq5_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 3iq5_validation.xml.gz | 23.9 KB | Display | |
Data in CIF | 3iq5_validation.cif.gz | 31.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iq/3iq5 ftp://data.pdbj.org/pub/pdb/validation_reports/iq/3iq5 | HTTPS FTP |
-Related structure data
Related structure data | 3iq6C 3m79C 3hniS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS domain: (Details: chain A,B,C,D, using restrain) | ||||||||
Details | THE ASYMMETRIC UNIT CONTAINS TWO DIMERIC HALVES (CHAINS A/C, AND CHAINS B/D) OF TWO TETRAMERS. THE GENERATING OF FULL TETRAMERS IS DESCRIBED IN REMARK 350 |
-Components
#1: Protein | Mass: 11701.123 Da / Num. of mol.: 4 Mutation: R34A, L38A, Q41W, K42S, K59H, D66W, V69I, D73H, K77H, T96C, R98C, Y101C Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0ABE7 #2: Chemical | ChemComp-HEM / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.48 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 25% PEG 400, 0.1M Bis-Tris, 0.15M Sodium chloride, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 30, 2009 Details: Flat collimating mirror, double crystal monochromator, toroid focusing mirror |
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. all: 27396 / Num. obs: 27287 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 2.05→2.16 Å / Redundancy: 5 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 1.5 / Num. unique all: 4021 / Rsym value: 0.448 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3HNI Resolution: 2.05→50 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.767 / σ(F): 3 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||
Solvent computation | Bsol: 56.116 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 89.34 Å2 / Biso mean: 37.552 Å2 / Biso min: 11.33 Å2
| ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→50 Å
| ||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||
Refine LS restraints NCS |
| ||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.05→2.07 Å
| ||||||||||||||||||||||||||||
Xplor file |
|