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Yorodumi- PDB-2o2i: Crystal structure of haloalkane dehalogenase Rv2579 from Mycobact... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2o2i | ||||||
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Title | Crystal structure of haloalkane dehalogenase Rv2579 from Mycobacterium tuberculosis complexed with 1,3-propandiol | ||||||
Components | Haloalkane dehalogenase 3 | ||||||
Keywords | HYDROLASE / haloalkane dehalogenase / Mycobacterium tuberculosis / Rv2579 / 1 / 3-propandiol / alpha/beta-hydrolase protein / TB Structural Genomics Consortium / TBSGC | ||||||
Function / homology | Function and homology information halogenated hydrocarbon catabolic process / haloalkane dehalogenase / haloalkane dehalogenase activity / peptidoglycan-based cell wall / hydrolase activity / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Mazumdar, P.A. / Hulecki, J. / Cherney, M.M. / Garen, C.R. / James, M.N.G. / TB Structural Genomics Consortium (TBSGC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of haloalkane dehalogenase Rv2579 from Mycobacterium tuberculosis complexed with 1,3-propandiol Authors: Mazumdar, P.A. / Hulecki, J. / Cherney, M.M. / Garen, C.R. / James, M.N.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2o2i.cif.gz | 77.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2o2i.ent.gz | 56.5 KB | Display | PDB format |
PDBx/mmJSON format | 2o2i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2o2i_validation.pdf.gz | 430.5 KB | Display | wwPDB validaton report |
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Full document | 2o2i_full_validation.pdf.gz | 431.4 KB | Display | |
Data in XML | 2o2i_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | 2o2i_validation.cif.gz | 23.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o2/2o2i ftp://data.pdbj.org/pub/pdb/validation_reports/o2/2o2i | HTTPS FTP |
-Related structure data
Related structure data | 1mj5S S: Starting model for refinement |
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Similar structure data | |
Other databases |
-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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-Components
#1: Protein | Mass: 33764.090 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: dhaA / Plasmid: pDEST-15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS References: UniProt: Q50642, UniProt: P9WMR9*PLUS, haloalkane dehalogenase |
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#2: Chemical | ChemComp-BR / |
#3: Chemical | ChemComp-PDO / |
#4: 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: 1.85 Å3/Da / Density % sol: 33.5 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 30% PEG 4000, 0.2M magnesium acetate, 0.1M Tris, 5% ethylene glycol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115879 | ||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 11, 2006 | ||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||
Radiation wavelength | Wavelength: 1.115879 Å / Relative weight: 1 | ||||||
Reflection | Resolution: 1.5→63.043 Å / Num. all: 40063 / Num. obs: 39855 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 10.1 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 5.2 | ||||||
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.193 / Mean I/σ(I) obs: 3.6 / Num. measured all: 15268 / Num. unique all: 5410 / Rsym value: 0.193 / % possible all: 92.9 |
-Phasing
Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1MJ5 Resolution: 1.5→36.35 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.11 / SU ML: 0.043 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.068 / ESU R Free: 0.071 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 9.054 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→36.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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