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Yorodumi- PDB-7rwx: Crystal structure of a Zn-bound RIDC1 variant in the presence of ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7rwx | ||||||||||||
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Title | Crystal structure of a Zn-bound RIDC1 variant in the presence of reductant | ||||||||||||
Components | Soluble cytochrome b562 | ||||||||||||
Keywords | METAL BINDING PROTEIN | ||||||||||||
Function / homology | Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / electron transfer activity / periplasmic space / iron ion binding / heme binding / HEME C / Soluble cytochrome b562 Function and homology information | ||||||||||||
Biological species | Escherichia coli (E. coli) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 | 7rwx.cif.gz | 70 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7rwx.ent.gz | 44.6 KB | Display | PDB format |
PDBx/mmJSON format | 7rwx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rw/7rwx ftp://data.pdbj.org/pub/pdb/validation_reports/rw/7rwx | HTTPS FTP |
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-Related structure data
Related structure data | 7rwuC 7rwvC 7rwwC 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
#1: Protein | Mass: 11657.113 Da / Num. of mol.: 2 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 #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | 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: 3.82 Å3/Da / Density % sol: 67.76 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 30% PEG400, 0.1 M HEPES, 0.2 M CaCl2 |
-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: Nov 11, 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: 1.6→80.69 Å / Num. obs: 27879 / % possible obs: 96.2 % / Redundancy: 4.1 % / Biso Wilson estimate: 36.04 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.042 / Rrim(I) all: 0.089 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 1.6→1.64 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.312 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 7175 / CC1/2: 0.898 / Rpim(I) all: 0.185 / Rrim(I) all: 0.366 / % possible all: 91.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2bc5 Resolution: 1.6→37.01 Å / SU ML: 0.2339 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 45.5369 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: 50.21 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→37.01 Å
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Refine LS restraints |
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LS refinement shell |
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