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- PDB-6q50: Structure of MPT-4, a mannose phosphorylase from Leishmania mexic... -

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Basic information

Entry
Database: PDB / ID: 6q50
TitleStructure of MPT-4, a mannose phosphorylase from Leishmania mexicana, in complex with phosphate ion
ComponentsMPT-4
KeywordsHYDROLASE / phosphorylase
Function / homologyMannosyltransferase/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 / PHOSPHATE ION / DUF1861 family protein
Function and homology information
Biological speciesLeishmania mexicana (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSobala, 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
OrganizationGrant numberCountry
Australian Research CouncilDP160100597 Australia
Australian Research CouncilDP180101957 Australia
Biotechnology and Biological Sciences Research CouncilBB/M011151 United Kingdom
European Research CouncilERC-2012-AdG-322942 United Kingdom
CitationJournal: 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
DepositionDec 6, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2021Group: Database references / Derived calculations
Category: pdbx_related_exp_data_set / pdbx_struct_conn_angle / struct_conn
Item: _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id ..._pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr2_auth_seq_id
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MPT-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7814
Polymers37,6011
Non-polymers1803
Water6,720373
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, SECMALS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area630 Å2
ΔGint-18 kcal/mol
Surface area13870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.366, 67.194, 96.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11A-506-

HOH

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Components

#1: Protein MPT-4


Mass: 37601.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania mexicana (strain MHOM/GT/2001/U1103) (eukaryote)
Strain: MHOM/GT/2001/U1103 / Gene: LMXM_10_1260 / Plasmid: pET28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E9ANE0
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 373 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 100 mM PCTP pH 7.0, 25% w/v PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.969 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.969 Å / Relative weight: 1
ReflectionResolution: 1.6→67.19 Å / Num. obs: 46829 / % possible obs: 100 % / Redundancy: 8 % / Biso Wilson estimate: 20.08 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.039 / Rrim(I) all: 0.111 / Net I/σ(I): 10.2
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 8 % / Rmerge(I) obs: 1.853 / Num. unique obs: 2286 / CC1/2: 0.459 / Rpim(I) all: 0.704 / Rrim(I) all: 1.985 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
DIALS1.8.1-g1afca60c-release-hotfix1data reduction
Aimless0.7.1data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B4W

2b4w


Resolution: 1.6→67.28 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.786 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20006 2360 5 %RANDOM
Rwork0.16048 ---
obs0.16241 44419 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.552 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å2-0 Å2-0 Å2
2---0.6 Å20 Å2
3---0.44 Å2
Refinement stepCycle: 1 / Resolution: 1.6→67.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2519 0 10 373 2902
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132651
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172398
X-RAY DIFFRACTIONr_angle_refined_deg1.7421.653588
X-RAY DIFFRACTIONr_angle_other_deg1.4351.585575
X-RAY DIFFRACTIONr_dihedral_angle_1_deg14.6695.337341
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.12221.736144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.44515432
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2161518
X-RAY DIFFRACTIONr_chiral_restr0.0890.2331
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023262
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02600
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0622.2131286
X-RAY DIFFRACTIONr_mcbond_other2.0632.211285
X-RAY DIFFRACTIONr_mcangle_it2.9543.3061608
X-RAY DIFFRACTIONr_mcangle_other2.9543.3091609
X-RAY DIFFRACTIONr_scbond_it3.1982.631364
X-RAY DIFFRACTIONr_scbond_other3.192.6271362
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8113.8081973
X-RAY DIFFRACTIONr_long_range_B_refined6.50427.822998
X-RAY DIFFRACTIONr_long_range_B_other6.38527.0432913
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 183 -
Rwork0.266 3227 -
obs--99.91 %

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