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- PDB-8drl: Zn(II)-bound B2 dimer (H60/H100/H104) formed in Cu(II)//Zn(II) (M... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8drl | ||||||
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Title | Zn(II)-bound B2 dimer (H60/H100/H104) formed in Cu(II)//Zn(II) (M1 // M2) condition | ||||||
![]() | Soluble cytochrome b562 | ||||||
![]() | METAL BINDING PROTEIN / Trinuclear / Selectivity | ||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Choi, T.S. / Tezcan, F.A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Design of a Flexible, Zn-Selective Protein Scaffold that Displays Anti-Irving-Williams Behavior. Authors: Choi, T.S. / 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 | ![]() | 48.4 KB | Display | ![]() |
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PDB format | ![]() | 25.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8drdC ![]() 8drfC ![]() 8drjC ![]() 8drmC ![]() 2bc5S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 11843.324 Da / Num. of mol.: 1 / Mutation: D60H, A100H, K104H Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-HEC / ![]() | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | ![]() Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.16 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: PEG3350 24%, CHES 100 mM |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 17, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.65→39.64 Å / Num. obs: 15118 / % possible obs: 98.97 % / Redundancy: 2 % / Biso Wilson estimate: 18.17 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.04037 / Rpim(I) all: 0.04037 / Rrim(I) all: 0.05709 / Net I/σ(I): 15.46 |
Reflection shell | Resolution: 1.65→1.709 Å / Rmerge(I) obs: 0.1227 / Mean I/σ(I) obs: 5.03 / Num. unique obs: 2910 / CC1/2: 0.961 / CC star: 0.99 / Rpim(I) all: 0.1227 / Rrim(I) all: 0.1736 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 2bc5 Resolution: 1.65→39.64 Å / SU ML: 0.1456 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.1901 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.58 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→39.64 Å
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Refine LS restraints |
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LS refinement shell |
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