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Yorodumi- PDB-4u9e: Crystal structure of the Zn-directed tetramer of the engineered c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4u9e | |||||||||
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Title | Crystal structure of the Zn-directed tetramer of the engineered cyt cb562 variant, A104/57G AB3 | |||||||||
Components | Soluble cytochrome b562 | |||||||||
Keywords | ELECTRON TRANSPORT / designed enzyme / Zn-coordinating protein / tetramer assembly | |||||||||
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: 2.8 Å | |||||||||
Authors | Tezcan, F.A. / Song, W.J. | |||||||||
Funding support | United States, 1items
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Citation | Journal: Science / Year: 2014 Title: A designed supramolecular protein assembly with in vivo enzymatic activity Authors: Song, W.J. / Tezcan, A.F. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4u9e.cif.gz | 39.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4u9e.ent.gz | 24.9 KB | Display | PDB format |
PDBx/mmJSON format | 4u9e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u9/4u9e ftp://data.pdbj.org/pub/pdb/validation_reports/u9/4u9e | HTTPS FTP |
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-Related structure data
Related structure data | 4u9dC 2bc5S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Symmetry | Point symmetry: (Schoenflies symbol: D2 (2x2 fold dihedral)) | |||||||||||||||||||||||||||
Components on special symmetry positions |
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-Components
#1: Protein | Mass: 11705.097 Da / Num. of mol.: 1 / Fragment: UNP residues 23-128 Mutation: R34A, L38A, Q41W, K42S, E57G, K59H, D66W, V69I, D73H, K77H, A89H, T96C, R98C, A100H, Y101C, K104A, Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cybC / Plasmid: pET20b(+) / Details (production host): kan+/amp- / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0ABE7 | ||||
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#2: Chemical | ChemComp-HEC / | ||||
#3: Chemical | ChemComp-CA / #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.46 Å3/Da / Density % sol: 64.47 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 27% (+/-)-2-methyl-2,4-pentanediol 400 in 100 mM Bis-Tris (pH 6.5) with 0.2M CaCl2 and 20 mM ampicillin |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.98 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 28, 2014 |
Radiation | 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→35.66 Å / Num. obs: 4159 / % possible obs: 98.9 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 22.2 |
Reflection shell | Resolution: 2.8→8.86 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.048 / Mean I/σ(I) obs: 22.2 / Rsym value: 0.168 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2BC5 Resolution: 2.8→35.66 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.89 / SU B: 18.305 / SU ML: 0.368 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.866 / ESU R Free: 0.379 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→35.66 Å
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Refine LS restraints |
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