+Open data
-Basic information
Entry | Database: PDB / ID: 3umc | ||||||
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Title | Crystal Structure of the L-2-Haloacid Dehalogenase PA0810 | ||||||
Components | haloacid dehalogenase | ||||||
Keywords | HYDROLASE / Haloacid dehalogenase-like hydrolase protein superfamily | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å | ||||||
Authors | Petit, P. / Chan, P.W.Y. / Savchenko, A. / Yakunin, A.F. / Edwards, E.A. / Pai, E.F. | ||||||
Citation | Journal: To be Published Title: Structural adaptations of L-2-haloacid dehalogenases that enable hydrolytic defluorination Authors: Chan, P.W.Y. / To, T.K.W. / Petit, P. / Tran, C. / Waelti, M. / Savchenko, A. / Yakunin, A.F. / Edwards, E.A. / Pai, E.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3umc.cif.gz | 200.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3umc.ent.gz | 168.4 KB | Display | PDB format |
PDBx/mmJSON format | 3umc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/um/3umc ftp://data.pdbj.org/pub/pdb/validation_reports/um/3umc | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 29039.936 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA0810 / Plasmid: p15TV-L / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9I5C9, (S)-2-haloacid dehalogenase #2: Chemical | ChemComp-CL / #3: Chemical | #4: 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: 2.46 Å3/Da / Density % sol: 49.96 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 20% PEG3350, 0.2 M diammonium citrate, cryoprotectant: Paratone N, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 1, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Rosenbaum-Rock high-resolution double-crystal Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.15→125.581 Å / Num. all: 60928 / Num. obs: 60928 / % possible obs: 99.9 % / Redundancy: 6.5 % / Rsym value: 0.061 / Net I/σ(I): 19.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.15→28.377 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.919 / Occupancy max: 1 / Occupancy min: 1 / SU B: 4.967 / SU ML: 0.131 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.236 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 83.35 Å2 / Biso mean: 30.4834 Å2 / Biso min: 4.14 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→28.377 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.206 Å / Total num. of bins used: 20
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