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Yorodumi- PDB-8px4: Structure of the PAS domain code by the LIC_11128 gene from Lepto... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8px4 | ||||||
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Title | Structure of the PAS domain code by the LIC_11128 gene from Leptospira interrogans serovar Copenhageni Fiocruz, solved at wavelength 3.09 A | ||||||
Components | Diguanylate cyclase | ||||||
Keywords | UNKNOWN FUNCTION / GGDEF family protein | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Leptospira interrogans serovar Copenhageni (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å | ||||||
Authors | El Omari, K. / Duman, R. / Mykhaylyk, V. / Orr, C. / Guzzo, C.R. / Owens, R.J. / 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 | 8px4.cif.gz | 145.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8px4.ent.gz | 115.3 KB | Display | PDB format |
PDBx/mmJSON format | 8px4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/px/8px4 ftp://data.pdbj.org/pub/pdb/validation_reports/px/8px4 | HTTPS FTP |
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-Related structure data
Related structure data | 8pwnC 8px0C 8px1C 8px5C 8px7C 8px9C 8pxcC 8pxgC 8pxhC 8pxjC 8pxkC 8pxlC 8pyvC 8pyzC 8pz4C 8pz5C 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 13441.053 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leptospira interrogans serovar Copenhageni (bacteria) Gene: FVE87_03295 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6G9EEG0 #2: 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: 2.39 Å3/Da / Density % sol: 48.63 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M BIS-Tris pH 5,5, 17% w/v PEG 10,000, and 0.1 M Ammonium acetate |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I23 / Wavelength: 3.09 Å |
Detector | Type: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Jul 13, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 3.09 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→72.28 Å / Num. obs: 12470 / % possible obs: 81.04 % / Redundancy: 49.2 % / Biso Wilson estimate: 64.86 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.08298 / Rpim(I) all: 0.0117 / Rrim(I) all: 0.08386 / Net I/σ(I): 41.69 |
Reflection shell | Resolution: 2.5→2.59 Å / Rmerge(I) obs: 1.433 / Mean I/σ(I) obs: 2.39 / Num. unique obs: 1065 / CC1/2: 0.636 / % possible all: 78.66 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.5→72.28 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.914 / SU B: 21.063 / SU ML: 0.215 / Cross valid method: THROUGHOUT / ESU R: 2.951 / ESU R Free: 0.374 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 72.629 Å2
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Refinement step | Cycle: 1 / Resolution: 2.5→72.28 Å
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Refine LS restraints |
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