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- PDB-2o6b: 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: 2o6b | ||||||
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Title | Crystal structure of the PA5185 protein from Pseudomonas Aeruginosa strain PAO1- new crystal form. | ||||||
![]() | THIOESTERASE | ||||||
![]() | HYDROLASE / THIOESTERASE | ||||||
Function / homology | Thioesterase-like superfamily / fatty acyl-CoA hydrolase activity / Thioesterase superfamily / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta / Uncharacterized protein![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chruszcz, M. / Koclega, K.D. / Evdokimova, E. / Cymborowski, M. / 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 | ![]() | 65.3 KB | Display | ![]() |
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PDB format | ![]() | 48.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 429.3 KB | Display | ![]() |
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Full document | ![]() | 435.5 KB | Display | |
Data in XML | ![]() | 12.7 KB | Display | |
Data in CIF | ![]() | 16 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2av9SC ![]() 2o5uC ![]() 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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1 | ![]()
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Unit cell |
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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 / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 1 / Auth seq-ID: 6 - 144 / Label seq-ID: 8 - 146
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Components
#1: Protein | Mass: 16675.775 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.24 Å3/Da / Density % sol: 61.99 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 25% PEG 3350, 0.01M HEPES pH 7.0, 0.1M Bis-Tris pH 5.5, 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: 3.2→50 Å / Num. all: 6998 / Num. obs: 6998 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.1 % / Rmerge(I) obs: 0.108 / Rsym value: 0.072 / Net I/σ(I): 18 |
Reflection shell | Resolution: 3.2→3.31 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.553 / Mean I/σ(I) obs: 1.8 / Num. unique all: 599 / Rsym value: 0.473 / % possible all: 83.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2AV9 Resolution: 3.21→25 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.892 / SU B: 22.951 / SU ML: 0.393 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.492 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. REFMAC 5.2.0005 AND COOT WERE USED FOR REFINEMENT.
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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: 88.361 Å2
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Refinement step | Cycle: LAST / Resolution: 3.21→25 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1061 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 3.21→3.294 Å / Total num. of bins used: 20
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