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- PDB-6wyn: Transition metal inhibition and structural refinement of the M. t... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6wyn | ||||||
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Title | Transition metal inhibition and structural refinement of the M. tuberculosis esterase, Rv0045c | ||||||
![]() | Possible hydrolase | ||||||
![]() | HYDROLASE / serine esterase / allosteric regulation / conformational change | ||||||
Function / homology | carboxylesterase / Alpha/beta hydrolase family / carboxylic ester hydrolase activity / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / hydrolase activity / Esterase Rv0045c![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Macbeth, M.R. / Johnson, R.J. / Hoops, G.C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Transition metal cation inhibition of Mycobacterium tuberculosis esterase RV0045C. Authors: Bowles, I.E. / Pool, E.H. / Lancaster, B.S. / Lawson, E.K. / Savas, C.P. / Kartje, Z.J. / Severinac, L. / Cho, D.H. / Macbeth, M.R. / Johnson, R.J. / Hoops, G.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 75.9 KB | Display | ![]() |
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PDB format | ![]() | 54.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 430.9 KB | Display | ![]() |
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Full document | ![]() | 432.7 KB | Display | |
Data in XML | ![]() | 14.4 KB | Display | |
Data in CIF | ![]() | 21.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6wymC ![]() 3p2mS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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: 35589.789 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 25618 / H37Rv / Gene: Rv0045c / Plasmid: pET-28 / Details (production host): KanR / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-CL / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.39 Å3/Da / Density % sol: 63.73 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 0.2 M MgCl2, 0.1 M Imidazole pH 7.4, 18% PEG 4000, 0.01 M spermidine, 1x10^-7 M ZnCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 18, 2018 | ||||||||||||||||||||||||||||||
Radiation | Monochromator: Kohzu HLD-4 Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.279 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.72→113.28 Å / Num. obs: 42576 / % possible obs: 83.5 % / Redundancy: 17 % / CC1/2: 0.997 / Rmerge(I) obs: 0.189 / Rpim(I) all: 0.045 / Rrim(I) all: 0.195 / Net I/σ(I): 11.2 / Num. measured all: 723975 / Scaling rejects: 5 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3P2M Resolution: 1.81→113.28 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.924 / SU B: 2.969 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.129 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 121.76 Å2 / Biso mean: 24.581 Å2 / Biso min: 7.04 Å2
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Refinement step | Cycle: final / Resolution: 1.81→113.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.81→1.855 Å / Rfactor Rfree error: 0
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