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Yorodumi- PDB-2wue: Crystal structure of S114A mutant of HsaD from Mycobacterium tube... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wue | ||||||
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Title | Crystal structure of S114A mutant of HsaD from Mycobacterium tuberculosis in complex with HOPODA | ||||||
Components | 2-HYDROXY-6-OXO-6-PHENYLHEXA-2,4-DIENOATE HYDROLASE BPHD | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information : / 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase / 4,5-9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase activity / 2,6-dioxo-6-phenylhexa-3-enoate hydrolase / 2,6-dioxo-6-phenylhexa-3-enoate hydrolase activity / biological process involved in interaction with host / steroid biosynthetic process / : / lipid catabolic process / peptidoglycan-based cell wall / plasma membrane Similarity search - Function | ||||||
Biological species | MYCOBACTERIUM TUBERCULOSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Lack, N.A. / Yam, K.C. / Lowe, E.D. / Horsman, G.P. / Owen, R. / Sim, E. / Eltis, L.D. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2010 Title: Characterization of a carbon-carbon hydrolase from Mycobacterium tuberculosis involved in cholesterol metabolism. Authors: Lack, N.A. / Yam, K.C. / Lowe, E.D. / Horsman, G.P. / Owen, R.L. / Sim, E. / Eltis, L.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wue.cif.gz | 230.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wue.ent.gz | 186.5 KB | Display | PDB format |
PDBx/mmJSON format | 2wue.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wue_validation.pdf.gz | 695.8 KB | Display | wwPDB validaton report |
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Full document | 2wue_full_validation.pdf.gz | 701.2 KB | Display | |
Data in XML | 2wue_validation.xml.gz | 26 KB | Display | |
Data in CIF | 2wue_validation.cif.gz | 37.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wu/2wue ftp://data.pdbj.org/pub/pdb/validation_reports/wu/2wue | HTTPS FTP |
-Related structure data
Related structure data | 2wudSC 2wufC 2wugC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: given Matrix: (0.031368, 0.999502, -0.003362), Vector: |
-Components
#1: Protein | Mass: 31899.389 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PT7-7 / Production host: Escherichia coli DH5[alpha] (bacteria) References: UniProt: P96851, UniProt: P9WNH5*PLUS, 2,6-dioxo-6-phenylhexa-3-enoate hydrolase #2: Chemical | #3: Chemical | ChemComp-KEK / ( | #4: Water | ChemComp-HOH / | Compound details | ENGINEERED | Sequence details | S114A MUTANT | |
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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: 2.35 Å3/Da / Density % sol: 47.63 % / Description: NONE |
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Crystal grow | pH: 7 Details: 200MM KSCN, 24% PET 3350, 100MM BIS-TRIS PROPANE PH7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9757 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 22, 2008 Details: KIRKPATRICK BAEZ BIMORPH MIRROR PAIR FOR HORIZONTAL AND VERTICAL FOCUSSING |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9757 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→40.66 Å / Num. obs: 55043 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Biso Wilson estimate: 21.1 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 16 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 5 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3.1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WUD Resolution: 1.8→36.34 Å / SU ML: 0.21 / σ(F): 2 / Phase error: 21.03 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.28 Å2 / ksol: 0.36 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→36.34 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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