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Yorodumi- PDB-5xzi: Crystal structure of the Zn-directed tetramer of the engineered c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xzi | |||||||||
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Title | Crystal structure of the Zn-directed tetramer of the engineered cyt cb562 variant, AB5 | |||||||||
Components | Soluble cytochrome b562 | |||||||||
Keywords | ELECTRON TRANSPORT / de novo protein | |||||||||
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 / Resolution: 2.65 Å | |||||||||
Authors | Song, W.J. / Tezcan, F.A. | |||||||||
Citation | Journal: J. Am. Chem. Soc. / Year: 2017 Title: Importance of Scaffold Flexibility/Rigidity in the Design and Directed Evolution of Artificial Metallo-beta-lactamases. Authors: Song, W.J. / Yu, J. / 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 | 5xzi.cif.gz | 35.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xzi.ent.gz | 25.9 KB | Display | PDB format |
PDBx/mmJSON format | 5xzi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xz/5xzi ftp://data.pdbj.org/pub/pdb/validation_reports/xz/5xzi | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 11822.221 Da / Num. of mol.: 1 Mutation: R34A, L38A, Q41W, K42S, K59H, D66W, V69I, D73H, K77H, E86D, A89E, Q93H, T96C, R98C, A100H, 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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#2: Chemical | ChemComp-HEC / | ||||
#3: Chemical | #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: 2.59 Å3/Da / Density % sol: 52.47 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 31.5% 2-methyl-2,4-pentanediol 400, 0.1M HEPES, pH 7.5, 0.2M MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 5, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.65→49.665 Å / Num. all: 3383 / Num. obs: 3383 / % possible obs: 91.5 % / Redundancy: 3.8 % / Rpim(I) all: 0.022 / Rrim(I) all: 0.045 / Rsym value: 0.039 / Net I/av σ(I): 9.7 / Net I/σ(I): 25.6 / Num. measured all: 12901 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Resolution: 2.65→49.665 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.892 / SU B: 14.287 / SU ML: 0.292 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.396 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 110.38 Å2 / Biso mean: 55.317 Å2 / Biso min: 12.46 Å2
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Refinement step | Cycle: final / Resolution: 2.65→49.665 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.65→2.719 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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