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Yorodumi- PDB-6wza: Ni-bound structure of an engineered metal-dependent protein trime... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6wza | |||||||||
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Title | Ni-bound structure of an engineered metal-dependent protein trimer, TriCyt1 | |||||||||
Components | Soluble cytochrome b562 | |||||||||
Keywords | METAL BINDING PROTEIN / four-helix bundle / metalloprotein trimer | |||||||||
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: 2.5 Å | |||||||||
Authors | Tezcan, F.A. / Kakkis, A. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2020 Title: Metal-Templated Design of Chemically Switchable Protein Assemblies with High-Affinity Coordination Sites. Authors: Kakkis, A. / Gagnon, D. / Esselborn, J. / Britt, R.D. / 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 | 6wza.cif.gz | 86.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wza.ent.gz | 64.3 KB | Display | PDB format |
PDBx/mmJSON format | 6wza.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6wza_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 6wza_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 6wza_validation.xml.gz | 18 KB | Display | |
Data in CIF | 6wza_validation.cif.gz | 23.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wz/6wza ftp://data.pdbj.org/pub/pdb/validation_reports/wz/6wza | HTTPS FTP |
-Related structure data
Related structure data | 6wyuC 6wz0C 6wz1C 6wz2C 6wz3C 6wz7C 6wzcC 6x7eC 6x8xC 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 on special symmetry positions |
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-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 11854.326 Da / Num. of mol.: 3 / Mutation: K59H, D66N, G70W, D73H, K77H, R98C, Y101C 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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-Non-polymers , 6 types, 121 molecules
#2: Chemical | #3: Chemical | ChemComp-NI / | #4: Chemical | ChemComp-NA / #5: Chemical | ChemComp-CL / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
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: 3.72 Å3/Da / Density % sol: 66.92 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 22.5% PEG 400, 0.2 M NaCl, 0.1 M HEPES (pH 7.5) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.23984 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 8, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.23984 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→39.3463 Å / Num. obs: 19138 / % possible obs: 99.71 % / Redundancy: 19.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.1416 / Rpim(I) all: 0.0331 / Rrim(I) all: 0.1455 / Net I/σ(I): 18.23 |
Reflection shell | Resolution: 2.5→2.589 Å / Rmerge(I) obs: 0.6877 / Num. unique obs: 1865 / CC1/2: 0.979 / Rpim(I) all: 0.1591 / Rrim(I) all: 0.7061 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2bc5 Resolution: 2.5→39.3463 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 32.48 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→39.3463 Å
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Refine LS restraints |
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LS refinement shell |
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