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Yorodumi- PDB-6x7e: Co-bound structure of an engineered protein trimer, TriCyt3, with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6x7e | |||||||||
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Title | Co-bound structure of an engineered protein trimer, TriCyt3, with delta isomerism at the hexahistidine coordination site | |||||||||
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: 1.9987 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 | 6x7e.cif.gz | 92.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6x7e.ent.gz | 68.4 KB | Display | PDB format |
PDBx/mmJSON format | 6x7e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6x7e_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 6x7e_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 6x7e_validation.xml.gz | 19.8 KB | Display | |
Data in CIF | 6x7e_validation.cif.gz | 27.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x7/6x7e ftp://data.pdbj.org/pub/pdb/validation_reports/x7/6x7e | HTTPS FTP |
-Related structure data
Related structure data | 6wyuC 6wz0C 6wz1C 6wz2C 6wz3C 6wz7C 6wzaC 6wzcC 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
-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, 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, 385 molecules
#2: Chemical | #3: Chemical | ChemComp-CO / | #4: Chemical | #5: Chemical | ChemComp-MG / #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: 2.52 Å3/Da / Density % sol: 51.3 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 25% PEG1500, 200 mM MgCl2, 100 mM TRIS (8.5) |
-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 8, 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: 1.9987→39.7039 Å / Num. obs: 23245 / % possible obs: 96.31 % / Redundancy: 3.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.0418 / Rpim(I) all: 0.02655 / Rrim(I) all: 0.04973 / Net I/σ(I): 23.76 |
Reflection shell | Resolution: 1.999→2.071 Å / Rmerge(I) obs: 0.09344 / Mean I/σ(I) obs: 9.79 / Num. unique obs: 2169 / CC1/2: 0.99 / Rpim(I) all: 0.06061 / Rrim(I) all: 0.1119 / % possible all: 90.83 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2bc5 Resolution: 1.9987→39.7039 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.43 / Phase error: 21.4 / 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: 1.9987→39.7039 Å
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Refine LS restraints |
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LS refinement shell |
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