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- PDB-6yv7: Mannosyltransferase PcManGT from Pyrobaculum calidifontis -

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Basic information

Entry
Database: PDB / ID: 6yv7
TitleMannosyltransferase PcManGT from Pyrobaculum calidifontis
Components(Glycosyl transferase, family 2) x 2
KeywordsTRANSFERASE / Glycosyltransferase / Membrane protein / Mannosyltransferase
Function / homology
Function and homology information


glycosyltransferase activity / metal ion binding
Similarity search - Function
Glycosyltransferase 2-like / Glycosyl transferase family 2 / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Glycosyl transferase, family 2
Similarity search - Component
Biological speciesPyrobaculum calidifontis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.7 Å
AuthorsDivne, C. / Rosaria, G.
Funding support Sweden, 3items
OrganizationGrant numberCountry
Swedish Research Council2011-5768 Sweden
Swedish Research Council2013-5717 Sweden
Swedish Research Council2017-03877 Sweden
CitationJournal: J.Mol.Biol. / Year: 2020
Title: A Transmembrane Crenarchaeal Mannosyltransferase Is Involved in N-Glycan Biosynthesis and Displays an Unexpected Minimal Cellulose-Synthase-like Fold.
Authors: Gandini, R. / Reichenbach, T. / Spadiut, O. / Tan, T.C. / Kalyani, D.C. / Divne, C.
History
DepositionApr 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Glycosyl transferase, family 2
B: Glycosyl transferase, family 2


Theoretical massNumber of molelcules
Total (without water)78,0882
Polymers78,0882
Non-polymers00
Water00
1
A: Glycosyl transferase, family 2


Theoretical massNumber of molelcules
Total (without water)39,1101
Polymers39,1101
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycosyl transferase, family 2


Theoretical massNumber of molelcules
Total (without water)38,9791
Polymers38,9791
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.449, 107.608, 163.572
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glycosyl transferase, family 2


Mass: 39109.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrobaculum calidifontis (strain JCM 11548 / VA1) (archaea)
Strain: JCM 11548 / VA1 / Gene: Pcal_0472 / Plasmid: pWaldo-GFPd / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A3MTD6
#2: Protein Glycosyl transferase, family 2


Mass: 38978.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrobaculum calidifontis (strain JCM 11548 / VA1) (archaea)
Strain: JCM 11548 / VA1 / Gene: Pcal_0472 / Plasmid: pWaldo-GFPd / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A3MTD6
Has protein modificationY

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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: 2.9 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 mM HEPES (pH 7.5), 20% PEG 4000, 10% isopropanol, 10 mM MnCl2 and 2% 1,2,3-heptanetriol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.06884 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 17, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.06884 Å / Relative weight: 1
ReflectionResolution: 2.7→49.08 Å / Num. obs: 48112 / % possible obs: 99.9 % / Redundancy: 7 % / CC1/2: 0.997 / Net I/σ(I): 12.2
Reflection shellResolution: 2.7→2.8 Å / Mean I/σ(I) obs: 2.5 / Num. unique obs: 4916 / CC1/2: 0.894 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XSCALEdata scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.7→49.079 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.52 / Phase error: 32.02
RfactorNum. reflection% reflection
Rfree0.2902 3738 7.77 %
Rwork0.2473 --
obs0.2505 48089 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→49.079 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5386 0 0 0 5386
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0145542
X-RAY DIFFRACTIONf_angle_d1.8787592
X-RAY DIFFRACTIONf_dihedral_angle_d20.6861986
X-RAY DIFFRACTIONf_chiral_restr0.083859
X-RAY DIFFRACTIONf_plane_restr0.011965
LS refinement shellResolution: 2.7→2.7342 Å
RfactorNum. reflection% reflection
Rfree0.3479 138 -
Rwork0.3341 1596 -
obs--99 %

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