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Yorodumi- PDB-7mk4: Co-bound crystal structure of the engineered cyt cb562 variant, DiCyt2 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7mk4 | |||||||||
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Title | Co-bound crystal structure of the engineered cyt cb562 variant, DiCyt2 | |||||||||
Components | Soluble cytochrome b562 | |||||||||
Keywords | METAL BINDING PROTEIN / Metal selectivity / Irving-Williams series | |||||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.27 Å | |||||||||
Authors | Choi, T.S. / Tezcan, F.A. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nature / Year: 2022 Title: Overcoming universal restrictions on metal selectivity by protein design. Authors: 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 | 7mk4.cif.gz | 77.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7mk4.ent.gz | 48.2 KB | Display | PDB format |
PDBx/mmJSON format | 7mk4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7mk4_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 7mk4_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 7mk4_validation.xml.gz | 14.5 KB | Display | |
Data in CIF | 7mk4_validation.cif.gz | 21.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mk/7mk4 ftp://data.pdbj.org/pub/pdb/validation_reports/mk/7mk4 | HTTPS FTP |
-Related structure data
Related structure data | 7lr5C 7lraC 7lrbC 7lrrC 7lrvC 7lv1C 7n4fC 7n4gC 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
#1: Protein | Mass: 11915.375 Da / Num. of mol.: 2 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: 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: 2.26 Å3/Da / Density % sol: 45.48 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.6 / Details: PEG1500 25%, NaCl 140 mM, pH 6.6 MES 100 mM |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å |
Detector | Type: APEX II CCD / Detector: CCD / Date: Jun 23, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.269→34.42 Å / Num. obs: 57551 / % possible obs: 99.79 % / Redundancy: 7.2 % / Biso Wilson estimate: 14 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.024 / Rrim(I) all: 0.072 / Net I/σ(I): 10 |
Reflection shell | Resolution: 1.269→1.315 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.847 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 5614 / CC1/2: 0.765 / Rpim(I) all: 0.429 / Rrim(I) all: 0.953 / % possible all: 98.86 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2bc5 Resolution: 1.27→34.42 Å / SU ML: 0.1663 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.6635 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: 19.01 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.27→34.42 Å
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Refine LS restraints |
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LS refinement shell |
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