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Yorodumi- PDB-5t02: Structural characterisation of mutant Asp39Ala of thioesterase (N... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5t02 | ||||||
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Title | Structural characterisation of mutant Asp39Ala of thioesterase (NmACH) from Neisseria meningitidis | ||||||
Components | Acyl-CoA hydrolase | ||||||
Keywords | HYDROLASE / Thioesterase / Nisseria meningitidis / 4HBT / Acyl-CoA thioesterase / Coenzyme A / GDP | ||||||
Function / homology | Function and homology information thiolester hydrolase activity / Hydrolases; Acting on ester bonds; Thioester hydrolases Similarity search - Function | ||||||
Biological species | Neisseria meningitidis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Khandokar, Y.B. / Srivastava, P. / Forwood, J.K. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2017 Title: Structural insights into GDP-mediated regulation of a bacterial acyl-CoA thioesterase. Authors: Khandokar, Y.B. / Srivastava, P. / Cowieson, N. / Sarker, S. / Aragao, D. / Das, S. / Smith, K.M. / Raidal, S.R. / Forwood, J.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5t02.cif.gz | 194.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5t02.ent.gz | 156.4 KB | Display | PDB format |
PDBx/mmJSON format | 5t02.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t0/5t02 ftp://data.pdbj.org/pub/pdb/validation_reports/t0/5t02 | HTTPS FTP |
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-Related structure data
Related structure data | 5szuC 5szvC 5szyC 5szzC 5v3aC 4ienS 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
#1: Protein | Mass: 17968.611 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria meningitidis (bacteria) Gene: ERS514298_01532, ERS514410_00397, ERS514534_01643, ERS514708_01580, ERS514851_00814 Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3)pLysS AG References: UniProt: A0A0Y5D4F5, Hydrolases; Acting on ester bonds; Thioester hydrolases #2: Chemical | ChemComp-GDP / #3: Chemical | ChemComp-COA / #4: Chemical | ChemComp-CL / |
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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: 4.67 Å3/Da / Density % sol: 73.69 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / Details: 0.4 M ammonium phosphate monobasic |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 17, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→39.79 Å / Num. obs: 49406 / % possible obs: 99.98 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 13.87 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.177 / Mean I/σ(I) obs: 5.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4IEN Resolution: 2.8→39.789 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.73
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→39.789 Å
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Refine LS restraints |
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LS refinement shell |
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