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Yorodumi- PDB-2w11: Structure of the L-2-haloacid dehalogenase from Sulfolobus tokodaii -
+Open data
-Basic information
Entry | Database: PDB / ID: 2w11 | ||||||
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Title | Structure of the L-2-haloacid dehalogenase from Sulfolobus tokodaii | ||||||
Components | 2-HALOALKANOIC ACID DEHALOGENASE | ||||||
Keywords | HYDROLASE / HALOACID DEHALOGENASE / HAD | ||||||
Function / homology | Function and homology information | ||||||
Biological species | SULFOLOBUS TOKODAII (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Rye, C.A. / Isupov, M.N. / Lebedev, A.A. / Littlechild, J.A. | ||||||
Citation | Journal: Extremophiles / Year: 2009 Title: Biochemical and Structural Studies of a L-Haloacid Dehalogenase from the Thermophilic Archaeon Sulfolobus Tokodaii. Authors: Rye, C.A. / Isupov, M.N. / Lebedev, A.A. / Littlechild, J.A. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2007 Title: An Order-Disorder Twin Crystal of L-2-Haloacid Dehalogenase from Sulfolobus Tokodaii Authors: Rye, C.A. / Isupov, M.N. / Lebedev, A.A. / Littlechild, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2w11.cif.gz | 103.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2w11.ent.gz | 79.8 KB | Display | PDB format |
PDBx/mmJSON format | 2w11.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w1/2w11 ftp://data.pdbj.org/pub/pdb/validation_reports/w1/2w11 | HTTPS FTP |
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-Related structure data
Related structure data | 2w43C 1qq5S C: citing same article (ref.) 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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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.99999, -0.00155, -0.0034), Vector: |
-Components
#1: Protein | Mass: 23982.600 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SULFOLOBUS TOKODAII (archaea) / Strain: 7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q96XE7, (S)-2-haloacid dehalogenase #2: Chemical | #3: 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: 1.96 Å3/Da / Density % sol: 37 % Description: THE CRYSTAL WAS TWINNED BY THE RETICULAR MEROHEDRY. THE DATA WERE DETWINNED USING THE ORIGINAL ALGORITHM AS DESCRIBED IN A SECONDARY REFERENCE |
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Crystal grow | Details: 0.1M HEPES, 20% PEG6000 PH7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.729 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 5, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.729 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→23.21 Å / Num. obs: 27770 / % possible obs: 97.6 % / Observed criterion σ(I): 0 / Redundancy: 3.48 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 16 |
Reflection shell | Resolution: 1.9→1.95 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 5.7 / % possible all: 75 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QQ5 Resolution: 1.9→23.21 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.31 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.154 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.55 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→23.21 Å
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Refine LS restraints |
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