+Open data
-Basic information
Entry | Database: PDB / ID: 2bng | ||||||
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Title | Structure of an M.tuberculosis LEH-like epoxide hydrolase | ||||||
Components | MB2760 | ||||||
Keywords | HYDROLASE / M.TUBERCULOSIS / EPOXIDE HYDROLASE / LIMONENE / STRUCTURAL PROTEOMICS IN EUROPE / SPINE / STRUCTURAL GENOMICS | ||||||
Function / homology | Function and homology information cholesterol-5,6-oxide hydrolase / cholesterol-5,6-oxide hydrolase activity / soluble epoxide hydrolase / epoxide metabolic process / epoxide hydrolase activity / plasma membrane Similarity search - Function | ||||||
Biological species | MYCOBACTERIUM TUBERCULOSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å | ||||||
Authors | Johansson, P. / Arand, M. / Unge, T. / Bergfors, T. / Jones, T.A. / Mowbray, S.L. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: Structure of an Atypical Epoxide Hydrolase from Mycobacterium Tuberculosis Gives Insights Into its Function. Authors: Johansson, P. / Unge, T. / Cronin, A. / Arand, M. / Bergfors, T. / Jones, T.A. / Mowbray, S.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bng.cif.gz | 167.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bng.ent.gz | 142.2 KB | Display | PDB format |
PDBx/mmJSON format | 2bng.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bn/2bng ftp://data.pdbj.org/pub/pdb/validation_reports/bn/2bng | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper:
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-Components
#1: Protein | Mass: 16751.623 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: ENDOGENOUS LIGAND OF UNKNOWN ORIGIN BOUND IN THE ACTIVE SITE Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: Q7TY00, UniProt: O33283*PLUS, limonene-1,2-epoxide hydrolase #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: 2.3 Å3/Da / Density % sol: 45 % |
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-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934 |
Detector | Type: ADSC CCD / Detector: CCD / Details: MIRRORS |
Radiation | Monochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→70.9 Å / Num. obs: 16247 / % possible obs: 100 % / Observed criterion σ(I): 3 / Redundancy: 21.2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 29 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 21.5 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 8.8 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.911 / Cross valid method: THROUGHOUT / ESU R: 0.681 / ESU R Free: 0.298 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.94 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
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Refine LS restraints |
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