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- PDB-2xu2: Crystal Structure of the hypothetical protein PA4511 from Pseudom... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2xu2 | |||||||||
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Title | Crystal Structure of the hypothetical protein PA4511 from Pseudomonas aeruginosa | |||||||||
![]() | UPF0271 PROTEIN PA4511 | |||||||||
![]() | UNKNOWN FUNCTION | |||||||||
Function / homology | ![]() 5-oxoprolinase (ATP-hydrolysing) / 5-oxoprolinase (ATP-hydrolyzing) activity / : / carbohydrate metabolic process / ATP binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / McMahon, S.A. / White, M.F. / Naismith, J.H. | |||||||||
![]() | ![]() 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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 107.2 KB | Display | ![]() |
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PDB format | ![]() | 83 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | 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 ![]() 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 ( |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() ![]() |
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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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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