+Open data
-Basic information
Entry | Database: PDB / ID: 8pz5 | ||||||
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Title | Structure of ThcOx, solved at wavelength 3.099 A | ||||||
Components | SagB-type dehydrogenase domain protein | ||||||
Keywords | OXIDOREDUCTASE / oxidase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Cyanothece sp. PCC 7425 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.2 Å | ||||||
Authors | Duman, R. / El Omari, K. / Mykhaylyk, V. / Orr, C. / Wagner, A. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Commun Chem / Year: 2023 Title: Experimental phasing opportunities for macromolecular crystallography at very long wavelengths. Authors: El Omari, K. / Duman, R. / Mykhaylyk, V. / Orr, C.M. / Latimer-Smith, M. / Winter, G. / Grama, V. / Qu, F. / Bountra, K. / Kwong, H.S. / Romano, M. / Reis, R.I. / Vogeley, L. / Vecchia, L. / ...Authors: El Omari, K. / Duman, R. / Mykhaylyk, V. / Orr, C.M. / Latimer-Smith, M. / Winter, G. / Grama, V. / Qu, F. / Bountra, K. / Kwong, H.S. / Romano, M. / Reis, R.I. / Vogeley, L. / Vecchia, L. / Owen, C.D. / Wittmann, S. / Renner, M. / Senda, M. / Matsugaki, N. / Kawano, Y. / Bowden, T.A. / Moraes, I. / Grimes, J.M. / Mancini, E.J. / Walsh, M.A. / Guzzo, C.R. / Owens, R.J. / Jones, E.Y. / Brown, D.G. / Stuart, D.I. / Beis, K. / Wagner, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8pz5.cif.gz | 425 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8pz5.ent.gz | 314.3 KB | Display | PDB format |
PDBx/mmJSON format | 8pz5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pz/8pz5 ftp://data.pdbj.org/pub/pdb/validation_reports/pz/8pz5 | HTTPS FTP |
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-Related structure data
Related structure data | 8pwnC 8px0C 8px1C 8px4C 8px5C 8px7C 8px9C 8pxcC 8pxgC 8pxhC 8pxjC 8pxkC 8pxlC 8pyvC 8pyzC 8pz4C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 52882.129 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cyanothece sp. PCC 7425 (bacteria) / Gene: Cyan7425_0520 / Production host: Escherichia coli (E. coli) / References: UniProt: B8HTZ1 #2: Chemical | 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: 3.19 Å3/Da / Density % sol: 61.44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.75 / Details: 1.0 M sodium citrate, 0.1 M CHES pH 7.75 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I23 / Wavelength: 3.099 Å |
Detector | Type: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Feb 8, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 3.099 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→77.82 Å / Num. obs: 39731 / % possible obs: 91.63 % / Redundancy: 25.8 % / Biso Wilson estimate: 134.59 Å2 / CC1/2: 0.999 / Net I/σ(I): 29.98 |
Reflection shell | Resolution: 3.2→3.315 Å / Num. unique obs: 1817 / CC1/2: 0.722 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 3.2→77.82 Å / SU ML: 0.5076 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.5201 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 140.18 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→77.82 Å
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Refine LS restraints |
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LS refinement shell |
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