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Yorodumi- PDB-1u0k: The structure of a Predicted Epimerase PA4716 from Pseudomonas ae... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1u0k | ||||||
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Title | The structure of a Predicted Epimerase PA4716 from Pseudomonas aeruginosa | ||||||
Components | gene product PA4716 | ||||||
Keywords | structural genomics / unknown function / sctructural genomics / MCSG / Pseudomonas aeruginosa / protein structure initiative / PSI / Midwest Center for Structural Genomics | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å | ||||||
Authors | Cuff, M.E. / Ginell, S.L. / Rotella, F.J. / Xu, X. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: TO BE PUBLISHED Title: The structure of hypothetical protein PA4716 from Pseudomonas aeruginosa Authors: Cuff, M.E. / Ginell, S.J. / Rotella, F.J. / Xu, X. / Savchenko, A. / Edwards, A. / Joachimiak, A. | ||||||
History |
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Remark 300 | BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). ...BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). THE BIOLOGICAL UNIT IS UNKNOWN. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1u0k.cif.gz | 136.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1u0k.ent.gz | 110.9 KB | Display | PDB format |
PDBx/mmJSON format | 1u0k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u0/1u0k ftp://data.pdbj.org/pub/pdb/validation_reports/u0/1u0k | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 31364.678 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA4716 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HV82 #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: 2.1 Å3/Da / Density % sol: 40.6 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: di-Ammonium Citrate, PEG 3350, sucrose, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 150 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.97959 Å |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Apr 19, 2004 / Details: SBC2 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97959 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. all: 75759 / Num. obs: 75759 / % possible obs: 98.18 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.5→1.57 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 5.74 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.5→91.29 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.273 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.08 / ESU R Free: 0.076 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.202 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→91.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20 /
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