[English] 日本語
Yorodumi- PDB-8drl: Zn(II)-bound B2 dimer (H60/H100/H104) formed in Cu(II)//Zn(II) (M... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8drl | ||||||
---|---|---|---|---|---|---|---|
Title | Zn(II)-bound B2 dimer (H60/H100/H104) formed in Cu(II)//Zn(II) (M1 // M2) condition | ||||||
Components | Soluble cytochrome b562 | ||||||
Keywords | METAL BINDING PROTEIN / Trinuclear / Selectivity | ||||||
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: 1.65 Å | ||||||
Authors | Choi, T.S. / Tezcan, F.A. | ||||||
Funding support | United States, 1items
| ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8drl.cif.gz | 48.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8drl.ent.gz | 25.5 KB | Display | PDB format |
PDBx/mmJSON format | 8drl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8drl_validation.pdf.gz | 2.5 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8drl_full_validation.pdf.gz | 2.5 MB | Display | |
Data in XML | 8drl_validation.xml.gz | 8.1 KB | Display | |
Data in CIF | 8drl_validation.cif.gz | 10.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dr/8drl ftp://data.pdbj.org/pub/pdb/validation_reports/dr/8drl | HTTPS FTP |
-Related structure data
Related structure data | 8drdC 8drfC 8drjC 8drmC 2bc5S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-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 | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-HEC / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.16 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: PEG3350 24%, CHES 100 mM |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.27159 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 17, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.27159 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→39.64 Å / Num. obs: 15118 / % possible obs: 98.97 % / Redundancy: 2 % / Biso Wilson estimate: 18.17 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.04037 / Rpim(I) all: 0.04037 / Rrim(I) all: 0.05709 / Net I/σ(I): 15.46 |
Reflection shell | Resolution: 1.65→1.709 Å / Rmerge(I) obs: 0.1227 / Mean I/σ(I) obs: 5.03 / Num. unique obs: 2910 / CC1/2: 0.961 / CC star: 0.99 / Rpim(I) all: 0.1227 / Rrim(I) all: 0.1736 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2bc5 Resolution: 1.65→39.64 Å / SU ML: 0.1456 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.1901 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.58 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→39.64 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|