+Open data
-Basic information
Entry | Database: PDB / ID: 2xt0 | ||||||
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Title | Dehalogenase DPpA from Plesiocystis pacifica SIR-I | ||||||
Components | HALOALKANE DEHALOGENASE | ||||||
Keywords | HYDROLASE / ALPHA-BETA HYDROLASE FOLD | ||||||
Function / homology | Function and homology information | ||||||
Biological species | PLESIOCYSTIS PACIFICA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Bogdanovic, X. / Palm, G.J. / Hinrichs, W. | ||||||
Citation | Journal: Appl.Microbiol.Biotechnol. / Year: 2011 Title: Cloning, Functional Expression, Biochemical Characterization, and Structural Analysis of a Haloalkane Dehalogenase from Plesiocystis Pacifica Sir-1. Authors: Hesseler, M. / Bogdanovic, X. / Hidalgo, A. / Berenguer, J. / Palm, G.J. / Hinrichs, W. / Bornscheuer, U.T. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2010 Title: Crystallization and Preliminary X-Ray Diffraction Studies of the Putative Haloalkane Dehalogenase Dppa from Plesiocystis Pacifica Sir-I. Authors: Bogdanovic, X. / Hesseler, M. / Palm, G.J. / Bornscheuer, U.T. / Hinrichs, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xt0.cif.gz | 138.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xt0.ent.gz | 109.4 KB | Display | PDB format |
PDBx/mmJSON format | 2xt0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xt0_validation.pdf.gz | 437 KB | Display | wwPDB validaton report |
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Full document | 2xt0_full_validation.pdf.gz | 437.8 KB | Display | |
Data in XML | 2xt0_validation.xml.gz | 15.5 KB | Display | |
Data in CIF | 2xt0_validation.cif.gz | 23.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xt/2xt0 ftp://data.pdbj.org/pub/pdb/validation_reports/xt/2xt0 | HTTPS FTP |
-Related structure data
Related structure data | 1edbS S: Starting model for refinement |
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Similar 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: 32624.227 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PLESIOCYSTIS PACIFICA (bacteria) / Strain: SIR-I / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 GOLD / References: UniProt: A6G7B1, haloalkane dehalogenase | ||
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#2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 53 % / Description: NONE |
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Crystal grow | pH: 6.5 / Details: 0.1 M MES PH 6.5, 1.8M (NH4)2SO4, 5% PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 |
Detector | Type: RIGAKU SATURN 92 / Detector: CCD / Date: May 4, 2009 / Details: OSMIC MULTILAYER OPTIC |
Radiation | Monochromator: OSMIC MULTILAYER OPTIC / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→38.68 Å / Num. obs: 25613 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 7 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.3 / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EDB Resolution: 1.9→67.31 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.93 / SU B: 8.419 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. THE NUMBER OF UNIQUE REFLECTIONS FOR REFINEMENT IS 25826 AND FOR DATA PROCESSING 25613. THIS IS DUE TO A DIFFERENT ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. THE NUMBER OF UNIQUE REFLECTIONS FOR REFINEMENT IS 25826 AND FOR DATA PROCESSING 25613. THIS IS DUE TO A DIFFERENT RESOLUTION USED FOR REFINEMENT (1.9 A) AND PROCESSING (1.95 A).
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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 mean: 20.519 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→67.31 Å
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