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Yorodumi- PDB-6q4y: Structure of MPT-2, a GDP-Man-dependent mannosyltransferase from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6q4y | |||||||||||||||
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Title | Structure of MPT-2, a GDP-Man-dependent mannosyltransferase from Leishmania mexicana, in complex with mannose | |||||||||||||||
Components | LmxM MPT-2 | |||||||||||||||
Keywords | TRANSFERASE | |||||||||||||||
Function / homology | Function and homology information 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 Similarity search - Domain/homology | |||||||||||||||
Biological species | Leishmania mexicana MHOM/GT/2001/U1103 (eukaryote) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | |||||||||||||||
Authors | 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 | Australia, United Kingdom, 4items
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Citation | Journal: Cell Host Microbe / Year: 2019 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6q4y.cif.gz | 145.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6q4y.ent.gz | 111.2 KB | Display | PDB format |
PDBx/mmJSON format | 6q4y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q4/6q4y ftp://data.pdbj.org/pub/pdb/validation_reports/q4/6q4y | HTTPS FTP |
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-Related structure data
Related structure data | 6q4wC 6q4xC 6q4zC 6q50SC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.5281/zenodo.4428651 / Data set type: diffraction image data 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 |
-Links
-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: 0 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 0 / Auth seq-ID: 23 - 320 / Label seq-ID: 43 - 340
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-Components
#1: Protein | Mass: 38093.246 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania mexicana MHOM/GT/2001/U1103 (eukaryote) Gene: LMXM_10_1240 / Plasmid: pET28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E9AND8 #2: Sugar | #3: Sugar | #4: 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 % sol: 33.81 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / Details: 200 mM trisodium citrate, 18-22% w/v PEG 3350 / PH range: 7.5 - 9.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 18, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→71.58 Å / Num. obs: 63306 / % possible obs: 100 % / Redundancy: 7.7 % / Biso Wilson estimate: 29.36 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.091 / Rrim(I) all: 0.091 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.943 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3333 / CC1/2: 0.379 / Rpim(I) all: 0.353 / Rrim(I) all: 1.009 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6Q50 Resolution: 1.7→71.58 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.194 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.109 / 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: 32.108 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→71.58 Å
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Refine LS restraints |
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