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- PDB-7rwu: Crystal structure of Ni-bound RIDC1 variant in the presence of re... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7rwu | ||||||||||||
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Title | Crystal structure of Ni-bound RIDC1 variant in the presence of reductant | ||||||||||||
![]() | Soluble cytochrome b562 | ||||||||||||
![]() | METAL BINDING PROTEIN | ||||||||||||
Function / homology | ![]() electron transport chain / periplasmic space / electron transfer activity / iron ion binding / heme binding Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Kakkis, A. / Golub, E. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Redox- and metal-directed structural diversification in designed metalloprotein assemblies. Authors: Kakkis, A. / Golub, E. / 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 | ![]() | 52.5 KB | Display | ![]() |
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PDB format | ![]() | 29.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.1 MB | Display | ![]() |
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Full document | ![]() | 2.1 MB | Display | |
Data in XML | ![]() | 9.3 KB | Display | |
Data in CIF | ![]() | 12.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7rwvC ![]() 7rwwC ![]() 7rwxC ![]() 7rwyC ![]() 7su2C ![]() 7tepC ![]() 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 11657.113 Da / Num. of mol.: 1 Mutation: R56A, L60A, Q63W, K64S, K81H, D88W, V91I, D95H, D96A, K99H, T118C, R120C, Y123C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 179 molecules ![](data/chem/img/NI.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/HEC.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/HEC.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-TRS / | #4: Chemical | ChemComp-HEC / | #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.91 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 45% MPD, 0.1 M Tris, 0.2 M MgCl2 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 21, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→42.15 Å / Num. obs: 25101 / % possible obs: 99.99 % / Redundancy: 68 % / Biso Wilson estimate: 18.96 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.011 / Rrim(I) all: 0.07 / Net I/σ(I): 58.1 |
Reflection shell | Resolution: 1.8→1.8 Å / Rmerge(I) obs: 0.191 / Num. unique obs: 1344 / CC1/2: 0.998 / Rpim(I) all: 0.032 / Rrim(I) all: 0.193 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2bc5 Resolution: 1.8→42.15 Å / SU ML: 0.1797 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 18.8368 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: 23.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→42.15 Å
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Refine LS restraints |
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LS refinement shell |
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