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- PDB-2o5u: Crystal structure of the PA5185 protein from Pseudomonas Aerugino... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2o5u | ||||||
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Title | Crystal structure of the PA5185 protein from Pseudomonas Aeruginosa strain PAO1- orthorhombic form (C222). | ||||||
![]() | Thioesterase | ||||||
![]() | HYDROLASE / putative thioesterese | ||||||
Function / homology | : / Thioesterase-like superfamily / fatty acyl-CoA hydrolase activity / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta / Uncharacterized protein![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chruszcz, M. / Wang, S. / Evdokimova, E. / Koclega, K.D. / Kudritska, M. / Savchenko, A. / Edwards, A. / Minor, W. | ||||||
![]() | ![]() Title: Function-biased choice of additives for optimization of protein crystallization - the case of the putative thioesterase PA5185 from Pseudomonas aeruginosa PAO1. Authors: Chruszcz, M. / Zimmerman, M.D. / Wang, S. / Koclega, K.D. / Zheng, H. / Evdokimova, E. / Kudritska, M. / Cymborowski, M. / Savchenko, A. / Edwards, A. / Minor, W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 99 KB | Display | ![]() |
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PDB format | ![]() | 75.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2av9SC ![]() 2o6bC ![]() 2o6tC ![]() 2o6uC 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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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / Refine code: 4
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Components
#1: Protein | Mass: 16551.654 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.9 Details: 20% PEG 3350, 0.1M Bis-Tris, 0.05M MES, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 21, 2005 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 41694 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Rmerge(I) obs: 0.091 / Rsym value: 0.069 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 1.9 / Num. unique all: 3678 / Rsym value: 0.393 / % possible all: 87.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2AV9 Resolution: 1.91→50 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.928 / SU B: 5.938 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.141 / ESU R Free: 0.131 / 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: 22.688 Å2
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Refinement step | Cycle: LAST / Resolution: 1.91→50 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 1036 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.91→1.955 Å / Total num. of bins used: 20
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