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Yorodumi- PDB-3qw0: Crystal structure of the Zn-RIDC1 complex stabilized by BMB crosslinks -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qw0 | ||||||
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Title | Crystal structure of the Zn-RIDC1 complex stabilized by BMB crosslinks | ||||||
Components | Cytochrome cb562 | ||||||
Keywords | OXIDOREDUCTASE / Four-helix bundle | ||||||
Function / homology | Cytochrome c/b562 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / PROTOPORPHYRIN IX CONTAINING FE / 1,1'-butane-1,4-diylbis(1H-pyrrole-2,5-dione) Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.84 Å | ||||||
Authors | Salgado, E.N. / Tezcan, F.A. | ||||||
Citation | Journal: Inorg.Chem. / Year: 2011 Title: Templated construction of a zn-selective protein dimerization motif. Authors: Salgado, E.N. / Brodin, J.D. / To, M.M. / 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 | 3qw0.cif.gz | 105.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qw0.ent.gz | 87.3 KB | Display | PDB format |
PDBx/mmJSON format | 3qw0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3qw0_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 3qw0_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 3qw0_validation.xml.gz | 27.7 KB | Display | |
Data in CIF | 3qw0_validation.cif.gz | 37.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qw/3qw0 ftp://data.pdbj.org/pub/pdb/validation_reports/qw/3qw0 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 11745.175 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) |
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-Non-polymers , 5 types, 438 molecules
#2: Chemical | ChemComp-HEM / #3: Chemical | #4: Chemical | ChemComp-ZN / #5: Chemical | #6: 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: 2.41 Å3/Da / Density % sol: 49.01 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 100 mM Bis-TRIS, 14% PEG 3350, 2.84 mM zinc chloride, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SEALED TUBE / Type: OTHER / Wavelength: 1.541 Å |
Detector | Type: APEX II CCD / Detector: CCD / Date: Sep 8, 2010 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.541 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→22.55 Å / Num. all: 40145 / Num. obs: 39905 / % possible obs: 99.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 1.84→1.88 Å / Redundancy: 3.15 % / Mean I/σ(I) obs: 3.19 / Num. unique all: 2514 / Rsym value: 0.3236 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.84→22.5 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.922 / WRfactor Rfree: 0.2403 / WRfactor Rwork: 0.1889 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8366 / SU B: 3.342 / SU ML: 0.102 / SU R Cruickshank DPI: 0.1555 / SU Rfree: 0.1506 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.151 / 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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 54.67 Å2 / Biso mean: 19.9313 Å2 / Biso min: 4.22 Å2
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Refinement step | Cycle: LAST / Resolution: 1.84→22.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.84→1.887 Å / Total num. of bins used: 20
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