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- PDB-3qvz: Crystal structure of the Zn-RIDC1 complex stabilized by BMOE cros... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3qvz | ||||||
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Title | Crystal structure of the Zn-RIDC1 complex stabilized by BMOE crosslinks cocrystallized in the presence of Cu(II) | ||||||
![]() | Cytochrome cb562 | ||||||
![]() | OXIDOREDUCTASE / Four-helix bundle | ||||||
Function / homology | Cytochrome c/b562 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / COPPER (II) ION / PROTOPORPHYRIN IX CONTAINING FE / 1,1'-ethane-1,2-diylbis(1H-pyrrole-2,5-dione)![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Salgado, E.N. / Tezcan, F.A. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 94 KB | Display | ![]() |
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PDB format | ![]() | 78.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 22.4 KB | Display | |
Data in CIF | ![]() | 27.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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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.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 31 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/ME7.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/CU.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ME7.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/CU.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-HEM / #3: Chemical | #4: Chemical | ChemComp-ZN / #5: Chemical | ChemComp-CU / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.25 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 100 mM HEPES, 12% PEG 3350, 2.46 mM copper sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 10, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.265 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.5→45.488 Å / Num. all: 13499 / Num. obs: 13499 / % possible obs: 97.9 % / Redundancy: 15.8 % / Rsym value: 0.12 / Net I/σ(I): 13.8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
Software |
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Refinement | Method to determine structure: ![]()
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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: 123.38 Å2 / Biso mean: 22.1402 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.64→42.86 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 821 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.64→2.707 Å / Total num. of bins used: 20
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