+
Open data
-
Basic information
Entry | Database: PDB / ID: 7rww | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of a Zn-bound RIDC1 variant | ||||||||||||
![]() | 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 | ![]()
| ||||||||||||
![]() | ![]() Title: Redox- and metal-directed structural diversification in designed metalloprotein assemblies. Authors: Kakkis, A. / Golub, E. / Choi, T.S. / Tezcan, F.A. | ||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 212.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 151.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 7rwuC ![]() 7rwvC ![]() 7rwxC ![]() 7rwyC ![]() 7su2C ![]() 7tepC ![]() 2bc5S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 11657.113 Da / Num. of mol.: 4 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.) ![]() ![]() ![]() ![]() |
---|
-Non-polymers , 6 types, 265 molecules 










#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-HEC / #4: Chemical | #5: Chemical | ChemComp-MRD / ( | #6: Chemical | ChemComp-EPE / | #7: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|---|
Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.55 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 45% MPD, 0.1 M HEPES, 0.2 M MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 7, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→80.85 Å / Num. obs: 40172 / % possible obs: 99.9 % / Redundancy: 14.8 % / Biso Wilson estimate: 22.14 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.032 / Rrim(I) all: 0.126 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 1.7→1.761 Å / Rmerge(I) obs: 0.809 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 3987 / CC1/2: 0.617 / Rpim(I) all: 0.341 / Rrim(I) all: 0.849 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 2bc5 Resolution: 1.7→35.96 Å / SU ML: 0.1775 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.5074 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.86 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→35.96 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|