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- PDB-5mm0: Dolichyl phosphate mannose synthase in complex with GDP-mannose a... -

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Basic information

Entry
Database: PDB / ID: 5mm0
TitleDolichyl phosphate mannose synthase in complex with GDP-mannose and Mn2+ (donor complex)
ComponentsDolichol monophosphate mannose synthase
KeywordsMEMBRANE PROTEIN / Dolichol phosphate mannose synthase / enzyme / integral membrane protein / protein glycosylation / GDP-mannose / manganese ion / donor complex
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-ALPHA-D-MANNOSE / : / Dolichol-phosphate mannosyltransferase
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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)44,5289
Polymers42,6851
Non-polymers1,8438
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-27 kcal/mol
Surface area18480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.670, 146.320, 95.090
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, 22 molecules

#2: Chemical ChemComp-GDD / GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE


Mass: 605.341 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H25N5O16P2
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#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.: 5 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 3.69 Å3/Da / Density % sol: 66.71 %
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-mannose, 5 mM MnCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.86 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.86 Å / Relative weight: 1
ReflectionResolution: 2.3→29.6 Å / Num. obs: 28132 / % possible obs: 98.7 % / Redundancy: 12.7 % / Net I/σ(I): 20.1
Reflection shellResolution: 2.3→2.4 Å / Mean I/σ(I) obs: 1.6 / CC1/2: 0.669 / Rsym value: 1.939 / % possible all: 99.5

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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: 2.3→29.599 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 34.71
RfactorNum. reflection% reflection
Rfree0.2575 1998 7.1 %
Rwork0.2189 --
obs0.2217 28128 98.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→29.599 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2865 0 121 14 3000
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113062
X-RAY DIFFRACTIONf_angle_d1.3784127
X-RAY DIFFRACTIONf_dihedral_angle_d15.2451146
X-RAY DIFFRACTIONf_chiral_restr0.054456
X-RAY DIFFRACTIONf_plane_restr0.006495
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.35750.48631380.39741808X-RAY DIFFRACTION97
2.3575-2.42120.4051340.35941828X-RAY DIFFRACTION97
2.4212-2.49250.36761410.33671813X-RAY DIFFRACTION98
2.4925-2.57290.37341470.31571833X-RAY DIFFRACTION98
2.5729-2.66480.3411410.27191837X-RAY DIFFRACTION98
2.6648-2.77140.29351390.26111848X-RAY DIFFRACTION99
2.7714-2.89740.32151440.25361826X-RAY DIFFRACTION98
2.8974-3.050.28271360.25011887X-RAY DIFFRACTION99
3.05-3.24090.33221380.26441863X-RAY DIFFRACTION99
3.2409-3.49080.28481490.23991869X-RAY DIFFRACTION99
3.4908-3.84140.26991460.21521880X-RAY DIFFRACTION100
3.8414-4.39570.25131430.20371910X-RAY DIFFRACTION100
4.3957-5.53220.21281430.18991927X-RAY DIFFRACTION100
5.5322-29.60090.21151590.18582001X-RAY DIFFRACTION100

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