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Yorodumi- PDB-7lrb: Ni-bound crystal structure of the engineered cyt cb562 variant, D... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7lrb | |||||||||
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Title | Ni-bound crystal structure of the engineered cyt cb562 variant, DiCyt2, crystallized in the presence of Ni(II) (M1) and Cu(II) (M2) | |||||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 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 | 7lrb.cif.gz | 73.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7lrb.ent.gz | 45.6 KB | Display | PDB format |
PDBx/mmJSON format | 7lrb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7lrb_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 7lrb_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 7lrb_validation.xml.gz | 13 KB | Display | |
Data in CIF | 7lrb_validation.cif.gz | 18.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lr/7lrb ftp://data.pdbj.org/pub/pdb/validation_reports/lr/7lrb | HTTPS FTP |
-Related structure data
Related structure data | 7lr5C 7lraC 7lrrC 7lrvC 7lv1C 7mk4C 7n4fC 7n4gC 2bc5S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-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 / Mutation: D60H, I67H, Q71H, T97H, A100H, K104H 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: 2.25 Å3/Da / Density % sol: 45.33 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: PEG1500 25%, Ammonium acetate 160 mM, pH 8.4 EPPS 100 mM |
-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: 1.59 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 4, 2020 |
Radiation | Monochromator: Si(111) and Si(220) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.59 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→41.63 Å / Num. obs: 20861 / % possible obs: 97.65 % / Redundancy: 26 % / Biso Wilson estimate: 17.17 Å2 / CC1/2: 0.676 / CC star: 0.898 / Rmerge(I) obs: 0.7359 / Rpim(I) all: 0.1447 / Rrim(I) all: 0.7509 / Net I/σ(I): 31.17 |
Reflection shell | Resolution: 1.78→1.844 Å / Redundancy: 21.6 % / Rmerge(I) obs: 0.7766 / Mean I/σ(I) obs: 6.16 / Num. unique obs: 1911 / CC1/2: 0.788 / CC star: 0.939 / Rpim(I) all: 0.1692 / Rrim(I) all: 0.7961 / % possible all: 91.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2bc5 Resolution: 1.78→41.63 Å / SU ML: 0.1874 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.2315 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: 19.86 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.78→41.63 Å
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Refine LS restraints |
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LS refinement shell |
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