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Yorodumi- PDB-7rwu: Crystal structure of Ni-bound RIDC1 variant in the presence of re... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7rwu | ||||||||||||
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Title | Crystal structure of Ni-bound RIDC1 variant in the presence of reductant | ||||||||||||
Components | Soluble cytochrome b562 | ||||||||||||
Keywords | METAL BINDING PROTEIN | ||||||||||||
Function / homology | Function and homology information electron transport chain / electron transfer activity / periplasmic space / iron ion binding / heme binding Similarity search - Function | ||||||||||||
Biological species | Escherichia coli (E. coli) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||||||||
Authors | Kakkis, A. / Golub, E. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Chem.Commun.(Camb.) / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7rwu.cif.gz | 52.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7rwu.ent.gz | 29.8 KB | Display | PDB format |
PDBx/mmJSON format | 7rwu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rw/7rwu ftp://data.pdbj.org/pub/pdb/validation_reports/rw/7rwu | HTTPS FTP |
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-Related structure data
Related structure data | 7rwvC 7rwwC 7rwxC 7rwyC 7su2C 7tepC 2bc5S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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.) Escherichia coli (E. coli) / Gene: cybC / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABE7 |
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-Non-polymers , 5 types, 179 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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