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- PDB-6q4w: Structure of MPT-1, a GDP-Man-dependent mannosyltransferase from ... -

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Basic information

Entry
Database: PDB / ID: 6q4w
TitleStructure of MPT-1, a GDP-Man-dependent mannosyltransferase from Leishmania mexicana
ComponentsLmxM MPT-1
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 (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. / 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 18, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Feb 17, 2021Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.3Jan 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-1
B: LmxM MPT-1


Theoretical massNumber of molelcules
Total (without water)78,0102
Polymers78,0102
Non-polymers00
Water10,917606
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: light scattering, SECMALS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint0 kcal/mol
Surface area25030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.478, 48.116, 73.887
Angle α, β, γ (deg.)94.48, 96.92, 110.29
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

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

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

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Components

#1: Protein LmxM MPT-1


Mass: 39005.078 Da / Num. of mol.: 2
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_1230 / Plasmid: pET28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E9AND7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 606 / 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: 2.07 Å3/Da / Density % sol: 40.7 % / Description: needles
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 12% w/v PEG 20K, 100 mM MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

Software
NameVersionClassification
REFMAC5.8.0238refinement
DIALS1.8.6-gc63d8697-releasedata reduction
Aimless0.7.1 : 27/03/18data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Q4Y

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
RfactorNum. reflection% reflectionSelection details
Rfree0.21339 3977 4.9 %RANDOM
Rwork0.14943 ---
obs0.15258 76774 94.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.002 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å2-0.6 Å2-1.59 Å2
2--0.57 Å2-1.73 Å2
3---0.12 Å2
Refinement stepCycle: 1 / Resolution: 1.55→72.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4852 0 0 606 5458
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0135039
X-RAY DIFFRACTIONr_bond_other_d0.0030.0174536
X-RAY DIFFRACTIONr_angle_refined_deg1.7671.646844
X-RAY DIFFRACTIONr_angle_other_deg1.4751.57910537
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2945640
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.98522.734256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.14815827
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5111522
X-RAY DIFFRACTIONr_chiral_restr0.0880.2656
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025717
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021101
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_it3.2461.7222494
X-RAY DIFFRACTIONr_mcbond_other3.2431.7222493
X-RAY DIFFRACTIONr_mcangle_it3.7712.63117
X-RAY DIFFRACTIONr_mcangle_other3.7712.63118
X-RAY DIFFRACTIONr_scbond_it4.2912.1392545
X-RAY DIFFRACTIONr_scbond_other4.2912.1382545
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0363.0673714
X-RAY DIFFRACTIONr_long_range_B_refined5.81822.4375637
X-RAY DIFFRACTIONr_long_range_B_other5.46121.7615483
X-RAY DIFFRACTIONr_rigid_bond_restr6.00239575
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 9688 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.552→1.592 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 345 -
Rwork0.182 5463 -
obs--92.07 %

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