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- PDB-6q4z: Structure of an inactive variant (D94N) of MPT-2, a GDP-Man-depen... -

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Basic information

Entry
Database: PDB / ID: 6q4z
TitleStructure of an inactive variant (D94N) of MPT-2, a GDP-Man-dependent mannosyltransferase from Leishmania mexicana, in complex with beta-1,2-mannobiose
ComponentsLmxM MPT-2 D94N
KeywordsTRANSFERASE
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 / Glycosyl hydrolase-like protein
Function and homology information
Biological speciesLeishmania mexicana MHOM/GT/2001/U1103 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsSobala, L.F. / Males, A. / Bastidas, L.M. / Ward, T. / Sernee, M.F. / Ralton, J.E. / Nero, T.L. / Kloehn, J. / Viera-Lara, M. / Stanton, L. ...Sobala, L.F. / Males, A. / Bastidas, L.M. / Ward, T. / Sernee, M.F. / Ralton, J.E. / Nero, T.L. / Kloehn, J. / Viera-Lara, M. / Stanton, L. / Cobbold, S. / Pires, D.E. / Hanssen, E. / Parker, M.W. / Ascher, D.B. / Williams, S.J. / McConville, M.J. / Davies, G.J.
Funding support Australia, United Kingdom, 5items
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
National Health and Medical Research Council (Australia)APP1072476 Australia
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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 17, 2021Group: Database references / Derived calculations / Structure summary
Category: chem_comp / pdbx_related_exp_data_set / struct_conn
Item: _chem_comp.pdbx_synonyms / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Jan 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LmxM MPT-2 D94N
B: LmxM MPT-2 D94N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,8694
Polymers76,1852
Non-polymers6852
Water8,629479
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: light scattering, SECMALS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint24 kcal/mol
Surface area24060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.389, 98.115, 105.621
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 14 - 320 / Label seq-ID: 34 - 340

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein LmxM MPT-2 D94N


Mass: 38092.262 Da / Num. of mol.: 2 / Mutation: D94N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania mexicana MHOM/GT/2001/U1103 (eukaryote)
Plasmid: pET28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E9AND8
#2: Polysaccharide beta-D-mannopyranose-(1-2)-alpha-D-mannopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-2DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a1122h-1a_1-5][a1122h-1b_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(2+1)][b-D-Manp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 479 / 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: 1.88 Å3/Da / Density % sol: 34.7 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 200 mM triammonium citrate pH 7.0, 18-22% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.5→71.89 Å / Num. obs: 92517 / % possible obs: 99.8 % / Redundancy: 7.6 % / Biso Wilson estimate: 19.59 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.039 / Rrim(I) all: 0.109 / Net I/σ(I): 8.1
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.26 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4023 / CC1/2: 0.629 / Rpim(I) all: 0.522 / Rrim(I) all: 1.368 / % possible all: 97.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
DIALS1.11.2-g01fb9e997-releasedata reduction
Aimless0.7.3data scaling
REFMAC5.8.0238phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Q4Y

6q4y


Resolution: 1.55→71.89 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.964 / SU B: 3.693 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.078 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18941 4283 5.1 %RANDOM
Rwork0.12683 ---
obs0.12992 79610 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 27.653 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20 Å2-0 Å2
2---0.54 Å20 Å2
3---0.07 Å2
Refinement stepCycle: 1 / Resolution: 1.55→71.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4812 0 46 479 5337
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0135069
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174565
X-RAY DIFFRACTIONr_angle_refined_deg1.5551.6566881
X-RAY DIFFRACTIONr_angle_other_deg1.3931.58710632
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5545627
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.77322.53249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.5515812
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2711520
X-RAY DIFFRACTIONr_chiral_restr0.0790.2655
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025673
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021127
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_it3.6462.6442461
X-RAY DIFFRACTIONr_mcbond_other3.6472.6432460
X-RAY DIFFRACTIONr_mcangle_it4.5773.9773073
X-RAY DIFFRACTIONr_mcangle_other4.5763.9773074
X-RAY DIFFRACTIONr_scbond_it4.63.1012608
X-RAY DIFFRACTIONr_scbond_other4.63.1012608
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5514.4993798
X-RAY DIFFRACTIONr_long_range_B_refined5.94831.7935570
X-RAY DIFFRACTIONr_long_range_B_other5.86231.3165466
X-RAY DIFFRACTIONr_rigid_bond_restr2.53639634
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 9099 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.551→1.591 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 318 -
Rwork0.213 5723 -
obs--98.08 %

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