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- PDB-3pgv: Crystal structure of a haloacid dehalogenase-like hydrolase (KPN_... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3pgv | ||||||
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Title | Crystal structure of a haloacid dehalogenase-like hydrolase (KPN_04322) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 2.39 A resolution | ||||||
![]() | haloacid dehalogenase-like hydrolase | ||||||
![]() | HYDROLASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Joint Center for Structural Genomics (JCSG) | ||||||
![]() | ![]() Title: Crystal structure of a haloacid dehalogenase-like hydrolase (KPN_04322) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 2.39 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 430.8 KB | Display | ![]() |
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PDB format | ![]() | 359.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 497.9 KB | Display | ![]() |
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Full document | ![]() | 506.5 KB | Display | |
Data in XML | ![]() | 42.5 KB | Display | |
Data in CIF | ![]() | 59.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Details | CRYSTAL PACKING SUGGESTS THE ASSIGNMENT OF A MONOMER AS THE POSSIBLE OLIGOMERIZATION STATE IN SOLUTION. |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 32998.426 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: MGH 78578 / Gene: yigL, KPN78578_42660, KPN_04322 / Plasmid: SpeedET / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 458 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-EPE / #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-EDO / #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE CONSTRUCT (RESIDUES 1-266) WAS EXPRESSED WITH AND CONTAINS A PURIFICATI |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.68 % Description: DATA WERE SCALED USING XSCALE WITH FRIEDEL PAIRS KEPT AS SEPARATE WHEN COMPUTING R-SYM, COMPLETENESS AND Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 | Details: 15.0% Glycerol, 8.50% iso-Propanol, 17.0% PEG-4000, 0.1M HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 10, 2008 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97849 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.39→46.778 Å / Num. obs: 48581 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 39.559 Å2 / Rmerge(I) obs: 0.123 / Net I/σ(I): 8.04 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Details: 1.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED ...Details: 1.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 2.PROTEIN ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.3.4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID (EPE), GLYCEROL (GOL), AND 1,2 ETHANEDIOL (EDO) FROM THE CRYSTALLIZATION AND CRYOGENIC CONDITIONS HAVE BEEN MODELED INTO THE STRUCTURE. 4.A METAL ION WITHIN COORDINATION DISTANCE OF THE SIDECHAINS OF ASP 8, ASP 214, THE CARBONYL OXYGEN OF ASP 10, AND OXYGEN ATOMS OF GLYCEROL, AND 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID. IN SOME RELATED STRUCTURES, THIS METAL ION IS MODELED AS CALCIUM, AND IN OTHER RELATED STRUCTURES, IT IS MODELED AS MAGNESIUM. HERE THE METAL ION IS MODELD AS CALCIUM BASED ON A BETTER FIT TO ELECTRON DENSITY MAPS THAN THAT FOR MAGNESIUM. 5. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION. 6. THE REFINEMENT WAS RESTRAINED AGAINST THE SAD PHASES.
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Displacement parameters | Biso max: 123.75 Å2 / Biso mean: 43.2808 Å2 / Biso min: 16.27 Å2
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Refinement step | Cycle: LAST / Resolution: 2.39→46.778 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.39→2.45 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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