+Open data
-Basic information
Entry | Database: PDB / ID: 8drj | ||||||
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Title | Apo B2 dimer (H60/H100/H104) formed in the presence of Cu(II) | ||||||
Components | (Soluble cytochrome b562) x 2 | ||||||
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: 2.4 Å | ||||||
Authors | Choi, T.S. / Tezcan, F.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2022 Title: Design of a Flexible, Zn-Selective Protein Scaffold that Displays Anti-Irving-Williams Behavior. 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 | 8drj.cif.gz | 69 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8drj.ent.gz | 40.6 KB | Display | PDB format |
PDBx/mmJSON format | 8drj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8drj_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8drj_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8drj_validation.xml.gz | 10.9 KB | Display | |
Data in CIF | 8drj_validation.cif.gz | 13.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dr/8drj ftp://data.pdbj.org/pub/pdb/validation_reports/dr/8drj | HTTPS FTP |
-Related structure data
Related structure data | 8drdC 8drfC 8drlC 8drmC 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: 11843.324 Da / Num. of mol.: 1 / Mutation: D60H, 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 | ||||||
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#2: Protein | Mass: 11828.354 Da / Num. of mol.: 1 / Mutation: D60H, 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 | ||||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.47 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 Details: PEG3350 25%, (NH4)2SO4 200 mM, Tris 100 mM, CuCl2 4 mM |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.23981 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 16, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.23981 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→44.86 Å / Num. obs: 7510 / % possible obs: 99.4 % / Redundancy: 1.9 % / Biso Wilson estimate: 23.97 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.03868 / Rpim(I) all: 0.03868 / Rrim(I) all: 0.05471 / Net I/σ(I): 11.32 |
Reflection shell | Resolution: 2.4→2.486 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.08279 / Mean I/σ(I) obs: 6.72 / Num. unique obs: 1383 / CC1/2: 0.971 / CC star: 0.993 / Rpim(I) all: 0.08279 / Rrim(I) all: 0.1171 / % possible all: 99.32 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2bc5 Resolution: 2.4→44.86 Å / SU ML: 0.3436 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.7032 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: 25.66 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→44.86 Å
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Refine LS restraints |
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LS refinement shell |
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