+Open data
-Basic information
Entry | Database: PDB / ID: 6wz7 | |||||||||
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Title | Mn-bound structure of a TriCyt3 variant | |||||||||
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: 2.3 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 | 6wz7.cif.gz | 91.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wz7.ent.gz | 66.9 KB | Display | PDB format |
PDBx/mmJSON format | 6wz7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6wz7_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 6wz7_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 6wz7_validation.xml.gz | 18.1 KB | Display | |
Data in CIF | 6wz7_validation.cif.gz | 24.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wz/6wz7 ftp://data.pdbj.org/pub/pdb/validation_reports/wz/6wz7 | HTTPS FTP |
-Related structure data
Related structure data | 6wyuC 6wz0C 6wz1C 6wz2C 6wz3C 6wzaC 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: 11796.407 Da / Num. of mol.: 3 Mutation: T31K, A35K, Q41K, D54A, K59I, H63V, I67E, V69A, G70W, Q71E, D73H, L76A, K77H, N80E, E81K, 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, 269 molecules
#2: Chemical | #3: Chemical | ChemComp-MN / | #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-CA / #6: 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: 4.35 Å3/Da / Density % sol: 71.73 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 45% MPD, 0.2 M calcium chloride, 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: SSRL / Beamline: BL9-2 / Wavelength: 1.4855 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 6, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.4855 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→35.3956 Å / Num. obs: 26625 / % possible obs: 98.27 % / Redundancy: 3.4 % / CC1/2: 1 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.0402 / Rrim(I) all: 0.07543 / Net I/σ(I): 13.95 |
Reflection shell | Resolution: 2.3→2.382 Å / Rmerge(I) obs: 0.3441 / Num. unique obs: 2615 / CC1/2: 0.863 / Rpim(I) all: 0.2197 / Rrim(I) all: 0.41 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2bc5 Resolution: 2.3→35.3956 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.61 / 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: 2.3→35.3956 Å
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Refine LS restraints |
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LS refinement shell |
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