+Open data
-Basic information
Entry | Database: PDB / ID: 7rww | ||||||||||||
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Title | Crystal structure of a Zn-bound RIDC1 variant | ||||||||||||
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: 1.7 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 | 7rww.cif.gz | 213.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7rww.ent.gz | 151.3 KB | Display | PDB format |
PDBx/mmJSON format | 7rww.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7rww_validation.pdf.gz | 5.1 MB | Display | wwPDB validaton report |
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Full document | 7rww_full_validation.pdf.gz | 5.1 MB | Display | |
Data in XML | 7rww_validation.xml.gz | 23.3 KB | Display | |
Data in CIF | 7rww_validation.cif.gz | 31.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rw/7rww ftp://data.pdbj.org/pub/pdb/validation_reports/rw/7rww | HTTPS FTP |
-Related structure data
Related structure data | 7rwuC 7rwvC 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
-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.) Escherichia coli (E. coli) / Gene: cybC / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABE7 |
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-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 / | |
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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: 2.07 Å3/Da / Density % sol: 40.55 % |
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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 |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979 Å |
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 |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
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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: 29.86 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→35.96 Å
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Refine LS restraints |
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LS refinement shell |
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