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Yorodumi- PDB-6dhz: Crystallographic octamer of a metal-free RIDC1 variant bearing tw... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6dhz | |||||||||
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Title | Crystallographic octamer of a metal-free RIDC1 variant bearing two disulfide bonded cysteines | |||||||||
Components | Soluble cytochrome b562 | |||||||||
Keywords | ELECTRON TRANSPORT / 4-helix bundle / engineered protein / metalloprotein | |||||||||
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: 2.8 Å | |||||||||
Authors | Tezcan, F.A. / Churchfield, L.A. | |||||||||
Funding support | United States, 1items
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Citation | Journal: J. Am. Chem. Soc. / Year: 2018 Title: Determining the Structural and Energetic Basis of Allostery in a De Novo Designed Metalloprotein Assembly. Authors: Churchfield, L.A. / Alberstein, R.G. / Williamson, L.M. / 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 | 6dhz.cif.gz | 101.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6dhz.ent.gz | 77.3 KB | Display | PDB format |
PDBx/mmJSON format | 6dhz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6dhz_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 6dhz_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 6dhz_validation.xml.gz | 17.1 KB | Display | |
Data in CIF | 6dhz_validation.cif.gz | 23.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dh/6dhz ftp://data.pdbj.org/pub/pdb/validation_reports/dh/6dhz | HTTPS FTP |
-Related structure data
Related structure data | 6dhyC 3iq6S 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 4 / Auth seq-ID: 1 - 106 / Label seq-ID: 1 - 106
NCS oper:
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-Components
#1: Protein | Mass: 11733.188 Da / Num. of mol.: 4 Mutation: R34A, A38A, Q41W, K42S, K59H, D66W, V69I, D73H, K77H, T96C, 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 #2: Chemical | ChemComp-HEC / #3: Chemical | ChemComp-CA / #4: Water | ChemComp-HOH / | |
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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: 2.77 Å3/Da / Density % sol: 55.54 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 15% 2-methyl-2,4-pentane diol (v/v), 33.3 mM Bis-Tris (pH 6.5), 66.7 mM CaCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 7, 2016 |
Radiation | Monochromator: Si(111) and Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→78.55 Å / Num. obs: 13669 / % possible obs: 99.7 % / Redundancy: 9 % / Rsym value: 0.088 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 5.8 % / Num. unique obs: 1915 / Rsym value: 0.469 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3IQ6 Resolution: 2.8→78.55 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.908 / SU B: 16.988 / SU ML: 0.326 / Cross valid method: THROUGHOUT / ESU R Free: 0.403 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.337 Å2
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Refinement step | Cycle: 1 / Resolution: 2.8→78.55 Å
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Refine LS restraints |
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