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- PDB-5mm1: Dolichyl phosphate mannose synthase in complex with GDP and dolic... -

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Basic information

Entry
Database: PDB / ID: 5mm1
TitleDolichyl phosphate mannose synthase in complex with GDP and dolichyl phosphate mannose
ComponentsDolichol monophosphate mannose synthase
KeywordsMEMBRANE PROTEIN / Dolichol phosphate mannose synthase / enzyme / integral membrane protein / protein glycosylation / product complex / GDP / dolichyl phosphate mannose
Function / homology
Function and homology information


dolichyl-phosphate beta-D-mannosyltransferase / dolichyl-phosphate beta-D-mannosyltransferase activity / dolichol phosphate mannose biosynthetic process / GPI anchor biosynthetic process / dolichol-linked oligosaccharide biosynthetic process / protein O-linked glycosylation via mannose / polysaccharide biosynthetic process / metal ion binding / plasma membrane
Similarity search - Function
GtrA-like protein / DPM1-like / GtrA/DPMS, transmembrane domain / Glycosyltransferase 2-like / Glycosyl transferase family 2 / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / dolichyl phosphate mannose / Dolichol-phosphate mannosyltransferase
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsGandini, R. / Reichenbach, T. / Tan, T.C. / Divne, C.
Funding support Sweden, 3items
OrganizationGrant numberCountry
Swedish Research Council2011-5768 Sweden
Swedish Research Council2013-5717 Sweden
Swedish Research Council2012-915 Sweden
CitationJournal: Nat Commun / Year: 2017
Title: Structural basis for dolichylphosphate mannose biosynthesis.
Authors: Gandini, R. / Reichenbach, T. / Tan, T.C. / Divne, C.
History
DepositionDec 8, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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: Dolichol monophosphate mannose synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1393
Polymers42,6851
Non-polymers1,4552
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area680 Å2
ΔGint-4 kcal/mol
Surface area18620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.110, 144.540, 96.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Dolichol monophosphate mannose synthase


Mass: 42684.809 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal hexa-histdine tag and TEV protease cleavage site precedes the protein sequences
Source: (gene. exp.) Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) (archaea)
Gene: PF0058 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U4M3
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-MJC / dolichyl phosphate mannose


Mass: 1011.439 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C61H103O9P

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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: 3.69 Å3/Da / Density % sol: 66.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M potassium chloride, 0.1 M trisodium citrate (pH 5.5), 37% (v/v) pentaerythritol propoxylate (5/4 PO/OH), 50 mM Hepes (pH 7.5), 150 mM NaCl, 10% (v/v) glycerol, 0.05% LDAO, 5 mM GDP- ...Details: 0.2 M potassium chloride, 0.1 M trisodium citrate (pH 5.5), 37% (v/v) pentaerythritol propoxylate (5/4 PO/OH), 50 mM Hepes (pH 7.5), 150 mM NaCl, 10% (v/v) glycerol, 0.05% LDAO, 5 mM GDP-mannose, 5 mM MgCl2, 0.25 mM C55 dolichyl phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.6→48.385 Å / Num. obs: 19735 / % possible obs: 99.6 % / Redundancy: 12.8 % / Net I/σ(I): 14
Reflection shellResolution: 2.6→2.7 Å / Mean I/σ(I) obs: 1.1 / Rsym value: 3.535 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MLZ

5mlz


Resolution: 2.6→48.39 Å / SU ML: 0.52 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 42.41
RfactorNum. reflection% reflection
Rfree0.303 1973 10 %
Rwork0.238 --
obs0.244 19726 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→48.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2791 0 99 0 2890
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082966
X-RAY DIFFRACTIONf_angle_d1.2174013
X-RAY DIFFRACTIONf_dihedral_angle_d18.5991162
X-RAY DIFFRACTIONf_chiral_restr0.043448
X-RAY DIFFRACTIONf_plane_restr0.005480
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5999-2.6650.48691490.43071226X-RAY DIFFRACTION99
2.665-2.7370.45891310.39721258X-RAY DIFFRACTION100
2.737-2.81750.4321420.36851243X-RAY DIFFRACTION100
2.8175-2.90850.47031440.37581241X-RAY DIFFRACTION100
2.9085-3.01240.44431260.37351284X-RAY DIFFRACTION100
3.0124-3.1330.43361440.36831235X-RAY DIFFRACTION99
3.133-3.27560.4581330.35681261X-RAY DIFFRACTION99
3.2756-3.44820.36531380.27921250X-RAY DIFFRACTION100
3.4482-3.66420.34231420.24481259X-RAY DIFFRACTION100
3.6642-3.9470.31291370.20781272X-RAY DIFFRACTION100
3.947-4.34390.24261490.19871272X-RAY DIFFRACTION100
4.3439-4.9720.25331370.18661294X-RAY DIFFRACTION100
4.972-6.2620.26481460.21821295X-RAY DIFFRACTION100
6.262-48.39340.25021550.19631363X-RAY DIFFRACTION100

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