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Yorodumi- PDB-7rwy: Crystal structure of a Fe-bound RIDC1 variant in the presence of ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7rwy | ||||||||||||
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Title | Crystal structure of a Fe-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 / periplasmic space / electron transfer activity / iron ion binding / heme binding Similarity search - Function | ||||||||||||
Biological species | Escherichia coli (E. coli) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 | 7rwy.cif.gz | 174.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7rwy.ent.gz | 123.4 KB | Display | PDB format |
PDBx/mmJSON format | 7rwy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7rwy_validation.pdf.gz | 4.2 MB | Display | wwPDB validaton report |
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Full document | 7rwy_full_validation.pdf.gz | 4.2 MB | Display | |
Data in XML | 7rwy_validation.xml.gz | 32.3 KB | Display | |
Data in CIF | 7rwy_validation.cif.gz | 42.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rw/7rwy ftp://data.pdbj.org/pub/pdb/validation_reports/rw/7rwy | HTTPS FTP |
-Related structure data
Related structure data | 7rwuC 7rwvC 7rwwC 7rwxC 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 11657.113 Da / Num. of mol.: 6 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, 250 molecules
#2: Chemical | ChemComp-HEC / #3: Chemical | #4: Chemical | ChemComp-FE / #5: Chemical | ChemComp-TRS / | #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: 2.29 Å3/Da / Density % sol: 46.36 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 40% PPG, 0.1 M Bis-Tris |
-Data collection
Diffraction | Mean temperature: 100 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: Apr 2, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→46.27 Å / Num. obs: 30358 / % possible obs: 99.1 % / Redundancy: 3.9 % / Biso Wilson estimate: 31.55 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.054 / Rrim(I) all: 0.11 / Net I/σ(I): 8 |
Reflection shell | Resolution: 1.9→2 Å / Num. unique obs: 4390 / CC1/2: 0.863 / Rpim(I) all: 0.216 / Rrim(I) all: 0.434 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2bc5 Resolution: 2.2→44.65 Å / SU ML: 0.3155 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.4362 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: 39.71 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→44.65 Å
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Refine LS restraints |
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LS refinement shell |
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