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- PDB-5xzj: Crystal structure of the Zn-directed tetramer of the engineered c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5xzj | |||||||||
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Title | Crystal structure of the Zn-directed tetramer of the engineered cyt cb562 variant, C96T/AB5 | |||||||||
![]() | Soluble cytochrome b562 | |||||||||
![]() | ELECTRON TRANSPORT / de novo protein | |||||||||
Function / homology | ![]() electron transport chain / periplasmic space / electron transfer activity / iron ion binding / heme binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Song, W.J. / Tezcan, F.A. | |||||||||
Funding support | ![]() ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 107 KB | Display | ![]() |
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PDB format | ![]() | 86.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 21.2 KB | Display | |
Data in CIF | ![]() | 30.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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Components
#1: Protein | Mass: 11820.182 Da / Num. of mol.: 4 Mutation: R34A, L38A, Q41W, K42S, K59H, D66W, V69I, D73H, K77H, E86D, A89E, Q93H, R98C, A100H, Y101C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-HEC / #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.79 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 45% 2-methyl-2,4-pentanediol 400, 0.1M HEPES, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 18, 2015 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.98→63.893 Å / Num. all: 35176 / Num. obs: 35176 / % possible obs: 99.9 % / Redundancy: 5.8 % / Rpim(I) all: 0.026 / Rrim(I) all: 0.064 / Rsym value: 0.059 / Net I/av σ(I): 10.6 / Net I/σ(I): 17.8 / Num. measured all: 203462 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Resolution: 1.98→63.89 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.105 / SU ML: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.162 / ESU R Free: 0.148 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: 107.04 Å2 / Biso mean: 37.062 Å2 / Biso min: 18.16 Å2
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Refinement step | Cycle: final / Resolution: 1.98→63.89 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Number: 1585 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.98→2.031 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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