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Yorodumi- PDB-2x3o: Crystal Structure of the Hypothetical Protein PA0856 from Pseudom... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2x3o | ||||||
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Title | Crystal Structure of the Hypothetical Protein PA0856 from Pseudomonas aeruginosa | ||||||
Components | HYPOTHETICAL PROTEIN PA0856Hypothesis | ||||||
Keywords | UNKNOWN FUNCTION | ||||||
Function / homology | Domain of unknown function DUF2059 / Uncharacterized protein conserved in bacteria (DUF2059) / DUF2059 domain-containing protein Function and homology information | ||||||
Biological species | PSEUDOMONAS AERUGINOSA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å | ||||||
Authors | Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / White, M.F. / Naismith, J.H. | ||||||
Citation | Journal: J.Struct.Funct.Genomics / Year: 2010 Title: The Scottish Structural Proteomics Facility: Targets, Methods and Outputs. Authors: Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Yan, X. / Kerou, M. / Weikart, N.D. / Kadi, N. / Sheikh, M.A. / Schmelz, S. / Dorward, M. / Zawadzki, M. / Cozens, C. / ...Authors: Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Yan, X. / Kerou, M. / Weikart, N.D. / Kadi, N. / Sheikh, M.A. / Schmelz, S. / Dorward, M. / Zawadzki, M. / Cozens, C. / Falconer, H. / Powers, H. / Overton, I.M. / Van Niekerk, C.A.J. / Peng, X. / Patel, P. / Garrett, R.A. / Prangishvili, D. / Botting, C.H. / Coote, P.J. / Dryden, D.T.F. / Barton, G.J. / Schwarz-Linek, U. / Challis, G.L. / Taylor, G.L. / White, M.F. / Naismith, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2x3o.cif.gz | 61.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2x3o.ent.gz | 49.3 KB | Display | PDB format |
PDBx/mmJSON format | 2x3o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x3/2x3o ftp://data.pdbj.org/pub/pdb/validation_reports/x3/2x3o | HTTPS FTP |
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-Related structure data
Related structure data | 2ivyC 2jg5C 2jg6C 2vw8C 2vxzC 2wj9C 2x0oC 2x3dC 2x3eC 2x3fC 2x3gC 2x3lC 2x3mC 2x3nC 2x48C 2x4gC 2x4hC 2x4iC 2x4jC 2x4kC 2x4lC 2x5cC 2x5dC 2x5fC 2x5gC 2x5hC 2x5pC 2x5qC 2x5rC 2x5tC 2x7bC 2x7iC 2xu2C C: citing same article (ref.) |
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Similar 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: 16789.639 Da / Num. of mol.: 2 / Fragment: RESIDUES 35-182 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PA01 / Plasmid: PDEST14 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q9I585 #2: Chemical | ChemComp-GOL / | #3: Chemical | ChemComp-CL / | #4: Water | ChemComp-HOH / | Sequence details | THE FINAL CONSTRUCT ENTERING CRYSTALLIZATION TRIALS WAS A TRUNCATED VERSION (RESIDUES 1-36 REMOVED) ...THE FINAL CONSTRUCT ENTERING CRYSTALLIZ | |
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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: 3.86 Å3/Da / Density % sol: 68.1 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 36.3% PEGMME 550, 0.1M SODIUM CACODYLATE PH 6.5, 0.16M DI-AMMONIUM PHOSPHATE. CRYSTALS WERE CRYOPROTECTED WITH 3.67% HEXANEDIOL IN THE ABOVE SOLUTION |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.8 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 12, 2008 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→29.14 Å / Num. obs: 10798 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 0 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.97 |
Reflection shell | Resolution: 2.9→2.97 Å / Redundancy: 2 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 2.22 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 2.9→29.14 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.866 / SU B: 18.571 / SU ML: 0.367 / Cross valid method: THROUGHOUT / ESU R: 0.766 / ESU R Free: 0.416 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 71.13 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→29.14 Å
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