+Open data
-Basic information
Entry | Database: PDB / ID: 6wzc | |||||||||
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Title | Ni-bound structure of an engineered protein trimer, TriCyt3 | |||||||||
Components | Soluble cytochrome b562 | |||||||||
Keywords | METAL BINDING PROTEIN / four-helix bundle / metalloprotein trimer | |||||||||
Function / homology | Function and homology information electron transfer activity / periplasmic space / iron ion binding / heme binding Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.195 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 | 6wzc.cif.gz | 42.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wzc.ent.gz | 26.3 KB | Display | PDB format |
PDBx/mmJSON format | 6wzc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wz/6wzc ftp://data.pdbj.org/pub/pdb/validation_reports/wz/6wzc | HTTPS FTP |
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-Related structure data
Related structure data | 6wyuC 6wz0C 6wz1C 6wz2C 6wz3C 6wz7C 6wzaC 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, 1 molecules A
#1: Protein | Mass: 11796.407 Da / Num. of mol.: 1 Mutation: T31K, A35K, Q41K, D54A, K59I, H63V, I67E, V69A, G70W, Q71E, D73H, L76A, K77H, N80K, 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 , 5 types, 115 molecules
#2: Chemical | ChemComp-HEC / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-CA / #5: Chemical | #6: Water | ChemComp-HOH / | |
-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: 4.34 Å3/Da / Density % sol: 71.66 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 25% PEG2000, 0.2 M CaCl2, 0.1 M Bis-Tris (pH 6.5) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.2398 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 6, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2398 Å / Relative weight: 1 |
Reflection | Resolution: 2.195→35.7108 Å / Num. obs: 10934 / % possible obs: 99.62 % / Redundancy: 12.7 % / CC1/2: 0.887 / Rmerge(I) obs: 0.7438 / Rpim(I) all: 0.1867 / Rrim(I) all: 0.7678 / Net I/σ(I): 2.96 |
Reflection shell | Resolution: 2.195→2.274 Å / Rmerge(I) obs: 0.5781 / Num. unique obs: 1068 / CC1/2: 0.887 / Rpim(I) all: 0.2183 / Rrim(I) all: 0.6193 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2bc5 Resolution: 2.195→35.7108 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 20.55 / 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: 2.195→35.7108 Å
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Refine LS restraints |
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LS refinement shell |
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