+Open data
-Basic information
Entry | Database: PDB / ID: 2w43 | ||||||
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Title | Structure of L-haloacid dehalogenase from S. tokodaii | ||||||
Components | HYPOTHETICAL 2-HALOALKANOIC ACID DEHALOGENASE | ||||||
Keywords | HYDROLASE / METABOLIC PROCESS | ||||||
Function / homology | Function and homology information | ||||||
Biological species | SULFOLOBUS TOKODAII (archaea) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.66 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2w43.cif.gz | 113.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2w43.ent.gz | 87.5 KB | Display | PDB format |
PDBx/mmJSON format | 2w43.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2w43_validation.pdf.gz | 460.3 KB | Display | wwPDB validaton report |
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Full document | 2w43_full_validation.pdf.gz | 466.3 KB | Display | |
Data in XML | 2w43_validation.xml.gz | 25.3 KB | Display | |
Data in CIF | 2w43_validation.cif.gz | 38.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w4/2w43 ftp://data.pdbj.org/pub/pdb/validation_reports/w4/2w43 | HTTPS FTP |
-Related structure data
Related structure data | 2w11C 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.92, -0.234, 0.315), Vector: |
-Components
#1: Protein | Mass: 23446.014 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, EC: 3.1.8.2 #2: Chemical | ChemComp-PO4 / #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: 2.24 Å3/Da / Density % sol: 45 % / Description: NONE |
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Crystal grow | Details: 0.1M MES, 20% PEG6000, PH6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS / Wavelength: 1.54 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 21, 2006 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.66→15 Å / Num. obs: 51594 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 30.6 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 28.8 |
Reflection shell | Resolution: 1.66→1.69 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 7.3 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QQ5 Resolution: 1.66→55.05 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.792 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.106 / 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: 22.48 Å2
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Refinement step | Cycle: LAST / Resolution: 1.66→55.05 Å
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