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- PDB-6q4w: Structure of MPT-1, a GDP-Man-dependent mannosyltransferase from ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6q4w | |||||||||||||||
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Title | Structure of MPT-1, a GDP-Man-dependent mannosyltransferase from Leishmania mexicana | |||||||||||||||
![]() | LmxM MPT-1 | |||||||||||||||
![]() | TRANSFERASE | |||||||||||||||
Function / homology | Mannosyltransferase/phosphorylase 1-like, Leishmania / Protein of unknown function (DUF1861) / Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Mainly Beta / Uncharacterized protein![]() | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Sobala, L.F. / Males, A. / Bastidas, L.M. / Ward, T. / Sernee, M.F. / Ralton, J.E. / Nero, T.L. / Cobbold, S. / Kloehn, J. / Viera-Lara, M. ...Sobala, L.F. / Males, A. / Bastidas, L.M. / Ward, T. / Sernee, M.F. / Ralton, J.E. / Nero, T.L. / Cobbold, S. / Kloehn, J. / Viera-Lara, M. / Stanton, L. / Hanssen, E. / Parker, M.W. / Williams, S.J. / McConville, M.J. / Davies, G.J. | |||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: A Family of Dual-Activity Glycosyltransferase-Phosphorylases Mediates Mannogen Turnover and Virulence in Leishmania Parasites. Authors: Sernee, M.F. / Ralton, J.E. / Nero, T.L. / Sobala, L.F. / Kloehn, J. / Vieira-Lara, M.A. / Cobbold, S.A. / Stanton, L. / Pires, D.E.V. / Hanssen, E. / Males, A. / Ward, T. / Bastidas, L.M. / ...Authors: Sernee, M.F. / Ralton, J.E. / Nero, T.L. / Sobala, L.F. / Kloehn, J. / Vieira-Lara, M.A. / Cobbold, S.A. / Stanton, L. / Pires, D.E.V. / Hanssen, E. / Males, A. / Ward, T. / Bastidas, L.M. / van der Peet, P.L. / Parker, M.W. / Ascher, D.B. / Williams, S.J. / Davies, G.J. / McConville, M.J. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 284.3 KB | Display | ![]() |
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PDB format | ![]() | 227.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6q4xC ![]() 6q4ySC ![]() 6q4zC ![]() 6q50C S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Experimental dataset #1 | Data reference: ![]() Details: Diffraction images used to solve the structures published in the article "A Family of Dual-Activity Glycosyltransferase-Phosphorylases Mediates Mannogen Turnover and Virulence in Leishmania Parasites" Metadata reference: 10.5281/zenodo.4428651 |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: CYS / Beg label comp-ID: CYS / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: _ / Auth seq-ID: 16 - 327 / Label seq-ID: 36 - 347
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Components
#1: Protein | Mass: 39005.078 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: MHOM/GT/2001/U1103 / Gene: LMXM_10_1230 / Plasmid: pET28a(+) / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.7 % / Description: needles |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 12% w/v PEG 20K, 100 mM MES pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 10, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→72.74 Å / Num. obs: 80753 / % possible obs: 94.5 % / Redundancy: 2.1 % / Biso Wilson estimate: 13.86 Å2 / CC1/2: 0.97 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.076 / Rrim(I) all: 0.119 / Net I/σ(I): 4.5 |
Reflection shell | Resolution: 1.55→1.58 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.357 / Num. unique obs: 3818 / CC1/2: 0.782 / Rpim(I) all: 0.304 / Rrim(I) all: 0.47 / % possible all: 90.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6Q4Y Resolution: 1.55→72.74 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.994 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.092 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.002 Å2
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Refinement step | Cycle: 1 / Resolution: 1.55→72.74 Å
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Refine LS restraints |
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