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- PDB-5e9u: Crystal structure of GtfA/B complex bound to UDP and GlcNAc -

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Basic information

Entry
Database: PDB / ID: 5e9u
TitleCrystal structure of GtfA/B complex bound to UDP and GlcNAc
Components
  • Glycosyltransferase Gtf1
  • Glycosyltransferase-stabilizing protein Gtf2
KeywordsTRANSFERASE/CHAPERONE / Glycosyltransferase / Accessory protein translocation / Complex / TRANSFERASE-CHAPERONE complex
Function / homology
Function and homology information


protein O-linked glycosylation via serine / protein N-acetylglucosaminyltransferase complex / protein O-linked glycosylation / Transferases; Glycosyltransferases; Hexosyltransferases / glycosyltransferase activity / regulation of protein stability / nucleotide binding / plasma membrane / cytoplasm
Similarity search - Function
Glycosyltransferase-stabilising protein GtfB / Glycosyltransferase GtfA / : / GtfA extended beta-sheet domain / Glycosyl transferase, family 1 / Glycosyl transferases group 1
Similarity search - Domain/homology
URIDINE-5'-DIPHOSPHATE / UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase stabilizing protein GtfB / UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase GtfA subunit
Similarity search - Component
Biological speciesStreptococcus gordonii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.84 Å
AuthorsChen, Y. / Rapoport, T.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM052586 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Mechanism of a cytosolic O-glycosyltransferase essential for the synthesis of a bacterial adhesion protein.
Authors: Chen, Y. / Seepersaud, R. / Bensing, B.A. / Sullam, P.M. / Rapoport, T.A.
History
DepositionOct 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.7Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycosyltransferase Gtf1
B: Glycosyltransferase-stabilizing protein Gtf2
C: Glycosyltransferase Gtf1
D: Glycosyltransferase-stabilizing protein Gtf2
E: Glycosyltransferase Gtf1
F: Glycosyltransferase-stabilizing protein Gtf2
G: Glycosyltransferase Gtf1
H: Glycosyltransferase-stabilizing protein Gtf2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)441,26016
Polymers439,9128
Non-polymers1,3488
Water00
1
A: Glycosyltransferase Gtf1
B: Glycosyltransferase-stabilizing protein Gtf2
C: Glycosyltransferase Gtf1
D: Glycosyltransferase-stabilizing protein Gtf2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,6308
Polymers219,9564
Non-polymers6744
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12810 Å2
ΔGint-56 kcal/mol
Surface area85300 Å2
MethodPISA
2
E: Glycosyltransferase Gtf1
F: Glycosyltransferase-stabilizing protein Gtf2
G: Glycosyltransferase Gtf1
H: Glycosyltransferase-stabilizing protein Gtf2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,6308
Polymers219,9564
Non-polymers6744
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12940 Å2
ΔGint-50 kcal/mol
Surface area85330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.975, 196.005, 215.673
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Glycosyltransferase Gtf1 / Glycosyltransferase GtfA


Mass: 58399.207 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus gordonii (bacteria) / Strain: M99 / Gene: gtf1, gtfA / Production host: Escherichia coli (E. coli)
References: UniProt: Q9AET5, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Protein
Glycosyltransferase-stabilizing protein Gtf2 / Glycosyltransferase chaperone GtfB / orf4


Mass: 51578.770 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus gordonii (bacteria) / Strain: M99 / Gene: gtf2, gtfB / Production host: Escherichia coli (E. coli) / References: UniProt: Q79T00
#3: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
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: 3.58 Å3/Da / Density % sol: 65.63 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 4000, magnesium chloride, Tris, glycyl-glycyl-glycine
PH range: 7.5 - 8.0

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.84→148.98 Å / Num. obs: 60983 / % possible obs: 100 % / Redundancy: 7.3 % / Biso Wilson estimate: 111.56 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.385 / Rpim(I) all: 0.166 / Net I/σ(I): 5.28 / Num. measured all: 448209
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Num. measured allNum. unique allCC1/2Rpim(I) all% possible allRmerge(I) obsMean I/σ(I) obs
3.84-4.057.56627987910.5810.87699.9
12.14-148.986.41352921080.9960.03299.50.07523.4

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5E9T

5e9t


Resolution: 3.84→94.481 Å / SU ML: 0.63 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 38.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3368 3821 3.3 %Random selection
Rwork0.2689 112079 --
obs0.2711 60748 99.54 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 309.3 Å2 / Biso mean: 115.4901 Å2 / Biso min: 31.83 Å2
Refinement stepCycle: final / Resolution: 3.84→94.481 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30864 0 84 0 30948
Biso mean--125.23 --
Num. residues----3793
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00531634
X-RAY DIFFRACTIONf_angle_d0.90142899
X-RAY DIFFRACTIONf_chiral_restr0.0544662
X-RAY DIFFRACTIONf_plane_restr0.0055609
X-RAY DIFFRACTIONf_dihedral_angle_d13.918841
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.84-3.88860.40491380.36244088422699
3.8886-3.93980.38451410.36464131427299
3.9398-3.99380.33511450.35594167431299
3.9938-4.05080.40491410.35374112425399
4.0508-4.11130.37641410.331141444285100
4.1113-4.17550.44471410.341241964337100
4.1755-4.2440.42271420.342641754317100
4.244-4.31720.37881380.319341354273100
4.3172-4.39570.3871460.304641744320100
4.3957-4.48020.3431410.286741774318100
4.4802-4.57170.31841430.278741124255100
4.5717-4.67110.33431420.276942124354100
4.6711-4.77970.31151430.261841304273100
4.7797-4.89920.36381430.271941204263100
4.8992-5.03170.27541430.270842204363100
5.0317-5.17980.3091420.28341404282100
5.1798-5.34690.37651360.288241564292100
5.3469-5.5380.35871430.284641444287100
5.538-5.75970.38271390.287941694308100
5.7597-6.02180.38111440.28141674311100
6.0218-6.33920.32941410.276741654306100
6.3392-6.73630.35491440.270541724316100
6.7363-7.25620.3291390.264641674306100
7.2562-7.98610.29961390.23941624301100
7.9861-9.14090.33051460.214641564302100
9.1409-11.51340.23651450.17634123426899
11.5134-94.50980.30281350.20314065420097

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