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Yorodumi- PDB-2xu2: Crystal Structure of the hypothetical protein PA4511 from Pseudom... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xu2 | |||||||||
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Title | Crystal Structure of the hypothetical protein PA4511 from Pseudomonas aeruginosa | |||||||||
Components | UPF0271 PROTEIN PA4511 | |||||||||
Keywords | UNKNOWN FUNCTION | |||||||||
Function / homology | Function and homology information 5-oxoprolinase (ATP-hydrolysing) / 5-oxoprolinase (ATP-hydrolyzing) activity / : / carbohydrate metabolic process / ATP binding Similarity search - Function | |||||||||
Biological species | PSEUDOMONAS AERUGINOSA (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 C, D. / Botting, 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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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xu2.cif.gz | 107.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xu2.ent.gz | 83 KB | Display | PDB format |
PDBx/mmJSON format | 2xu2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xu2_validation.pdf.gz | 431.1 KB | Display | wwPDB validaton report |
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Full document | 2xu2_full_validation.pdf.gz | 432.8 KB | Display | |
Data in XML | 2xu2_validation.xml.gz | 11.7 KB | Display | |
Data in CIF | 2xu2_validation.cif.gz | 15.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xu/2xu2 ftp://data.pdbj.org/pub/pdb/validation_reports/xu/2xu2 | HTTPS FTP |
-Related structure data
Related structure data | 2ivyC 2jg5C 2jg6C 2vw8C 2vxzC 2wj9C 2x0oC 2x3dC 2x3eC 2x3fC 2x3gC 2x3lC 2x3mC 2x3nC 2x3oC 2x48C 2x4gC 2x4hC 2x4iC 2x4jC 2x4kC 2x4lC 2x5cC 2x5dC 2x5fC 2x5gC 2x5hC 2x5pC 2x5qC 2x5rC 2x5tC 2x7bC 2x7iC 2dfaS S: Starting model for refinement 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: 27195.926 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-251 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Plasmid: PDEST14 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: Q9HVR0 |
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#2: Chemical | ChemComp-CIT / |
#3: Water | ChemComp-HOH / |
Sequence details | DUE TO CLONING THE FIRST M IS REMOVED AND REPLACED BY GA |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.5 % / Description: NONE |
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Crystal grow | pH: 9 Details: 42.4% PEGMME550, 0.13 M AMMONIUM CITRATE, 0.1M CHES, PH9.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Aug 9, 2008 / Details: SI (III) |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→21.26 Å / Num. obs: 10668 / % possible obs: 98.6 % / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 21.4 |
Reflection shell | Resolution: 2.3→2.36 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.4 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2DFA Resolution: 2.3→21.26 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.93 / SU B: 14.808 / SU ML: 0.181 / Cross valid method: THROUGHOUT / ESU R: 0.359 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES WITH TLS ADDED. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.515 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→21.26 Å
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Refine LS restraints |
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