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- PDB-5mlz: Dolichyl phosphate mannose synthase in complex with GDP and Mg2+ -

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Basic information

Entry
Database: PDB / ID: 5mlz
TitleDolichyl phosphate mannose synthase in complex with GDP and Mg2+
ComponentsDolichol monophosphate mannose synthase
KeywordsMEMBRANE PROTEIN / Dolichol phosphate mannose synthase / enzyme / integral membrane protein / protein glycosylation
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 / Dolichol-phosphate mannosyltransferase
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2 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 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dolichol monophosphate mannose synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,79411
Polymers42,6851
Non-polymers2,10910
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-17 kcal/mol
Surface area18540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.870, 146.210, 95.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 67 molecules

#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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 3.71 Å3/Da / Density % sol: 66.84 %
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, 5 mM MgCl2

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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: Sep 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2→42.95 Å / Num. obs: 43116 / % possible obs: 99.8 % / Redundancy: 13.3 % / Biso Wilson estimate: 46.5 Å2 / Net I/σ(I): 29.2
Reflection shellResolution: 2→2.1 Å / Mean I/σ(I) obs: 2.2 / CC1/2: 0.876 / Rsym value: 1.21 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
autoSHARPphasing
RefinementMethod to determine structure: MIR / Resolution: 2→41.016 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31.3
RfactorNum. reflection% reflection
Rfree0.2571 1995 4.63 %
Rwork0.241 --
obs0.2418 43104 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→41.016 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2864 0 142 57 3063
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053079
X-RAY DIFFRACTIONf_angle_d1.0514141
X-RAY DIFFRACTIONf_dihedral_angle_d15.3121176
X-RAY DIFFRACTIONf_chiral_restr0.033451
X-RAY DIFFRACTIONf_plane_restr0.004494
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.05010.36721360.3662888X-RAY DIFFRACTION99
2.0501-2.10550.36761440.33032882X-RAY DIFFRACTION99
2.1055-2.16750.3371430.29472895X-RAY DIFFRACTION100
2.1675-2.23740.33881260.27542904X-RAY DIFFRACTION100
2.2374-2.31740.34111530.27622919X-RAY DIFFRACTION100
2.3174-2.41020.34041360.26632908X-RAY DIFFRACTION100
2.4102-2.51990.2611390.26712948X-RAY DIFFRACTION100
2.5199-2.65270.25021510.26052885X-RAY DIFFRACTION100
2.6527-2.81880.31891370.25752938X-RAY DIFFRACTION100
2.8188-3.03640.29891410.25592935X-RAY DIFFRACTION100
3.0364-3.34190.25341540.26382941X-RAY DIFFRACTION100
3.3419-3.82510.28551340.2432971X-RAY DIFFRACTION100
3.8251-4.81810.23381470.223000X-RAY DIFFRACTION100
4.8181-41.0250.20441540.20963095X-RAY DIFFRACTION100

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