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- PDB-6yv8: Mannosyltransferase PcManGT from Pyrobaculum calidifontis in comp... -

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Basic information

Entry
Database: PDB / ID: 6yv8
TitleMannosyltransferase PcManGT from Pyrobaculum calidifontis in complex with GDP and Mn2+
Components(Glycosyl transferase, family 2) x 2
KeywordsTRANSFERASE / Glycosyltransferase Membrane protein Mannosyltransferase
Function / homologyGlycosyltransferase 2-like / Glycosyl transferase family 2 / Nucleotide-diphospho-sugar transferases / transferase activity / metal ion binding / GUANOSINE-5'-DIPHOSPHATE / : / Glycosyl transferase, family 2
Function and homology information
Biological speciesPyrobaculum calidifontis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.6 Å
AuthorsDivne, C. / Gandini, R.
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 / Derived calculations / Category: citation / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id
Revision 1.2Oct 9, 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 / _pdbx_entry_details.has_protein_modification

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,0856
Polymers78,0882
Non-polymers9964
Water00
1
A: Glycosyl transferase, family 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6083
Polymers39,1101
Non-polymers4982
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycosyl transferase, family 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4773
Polymers38,9791
Non-polymers4982
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.998, 107.644, 164.418
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: Plasmid / Details (production host): 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: Plasmid / Details (production host): pWaldo-GFPd / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A3MTD6
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
Has ligand of interestN
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: 2.96 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: Diamond / Beamline: I24 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→48.84 Å / Num. obs: 28580 / % possible obs: 99.6 % / Redundancy: 12.1 % / CC1/2: 0.998 / Net I/σ(I): 13.2
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 9.6 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2953 / CC1/2: 0.501 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.6→48.709 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2795 1999 7 %
Rwork0.2329 --
obs0.2362 28575 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→48.709 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5386 0 58 0 5444
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125602
X-RAY DIFFRACTIONf_angle_d1.4987686
X-RAY DIFFRACTIONf_dihedral_angle_d20.7962008
X-RAY DIFFRACTIONf_chiral_restr0.081867
X-RAY DIFFRACTIONf_plane_restr0.012967
LS refinement shellResolution: 2.6→2.665 Å
RfactorNum. reflection% reflection
Rfree0.4469 136 -
Rwork0.3939 1800 -
obs--97 %

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