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- PDB-1pnv: Crystal Structure of TDP-epi-Vancosaminyltransferase GtfA in comp... -

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Basic information

Entry
Database: PDB / ID: 1pnv
TitleCrystal Structure of TDP-epi-Vancosaminyltransferase GtfA in complexes with TDP and Vancomycin
Components
  • GLYCOSYLTRANSFERASE GTFA
  • VANCOMYCIN
KeywordsTRANSFERASE/ANTIBIOTIC / GT-B GLYCOSYLTRANSFERASE / ROSSMANN FOLD / GLYCOPEPTIDE / ANTIBIOTIC / TRANSFERASE-ANTIBIOTIC COMPLEX
Function / homology
Function and homology information


chloroorienticin B synthase / vancomycin biosynthetic process / UDP-glycosyltransferase activity / hexosyltransferase activity / : / carbohydrate metabolic process
Similarity search - Function
Glycosyltransferase family 28, N-terminal domain / Glycosyltransferase family 28 N-terminal domain / Erythromycin biosynthesis protein CIII-like, central / : / Erythromycin biosynthesis protein CIII-like, C-terminal domain / UDP-glucuronosyl/UDP-glucosyltransferase / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Vancomycin / THYMIDINE-5'-DIPHOSPHATE / : / dTDP-epi-vancosaminyltransferase
Similarity search - Component
Biological speciesAMYCOLATOPSIS ORIENTALIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsMulichak, A.M. / Losey, H.C. / Lu, W. / Wawrzak, Z. / Walsh, C.T. / Garavito, R.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Structure of the Tdp-Epi-Vancosaminyltransferase Gtfa from the Chloroeremomycin Biosynthetic Pathway.
Authors: Mulichak, A.M. / Losey, H.C. / Lu, W. / Wawrzak, Z. / Walsh, C.T. / Garavito, R.M.
History
DepositionJun 13, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2003Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary
Revision 1.4Dec 12, 2012Group: Other
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_poly / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLYCOSYLTRANSFERASE GTFA
B: GLYCOSYLTRANSFERASE GTFA
C: VANCOMYCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,4225
Polymers86,6973
Non-polymers7262
Water1,54986
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-28.1 kcal/mol
Surface area31340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.170, 153.170, 100.640
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsThe biological assembly is a monomer.

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Components

#1: Protein GLYCOSYLTRANSFERASE GTFA


Mass: 42773.398 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AMYCOLATOPSIS ORIENTALIS (bacteria) / Gene: GTFA / Plasmid: PET22B / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P96558
#2: Protein/peptide VANCOMYCIN


Type: Glycopeptide / Class: Antibiotic / Mass: 1149.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: VANCOMYCIN IS A TRICYCLIC GLYCOPEPTIDE, GLYCOSYLATED BY A DISACCHARIDE (RESIDUES 8 AND 9) ON RESIDUE 4.
Source: (natural) AMYCOLATOPSIS ORIENTALIS (bacteria) / References: NOR: NOR00681, Vancomycin
#3: Polysaccharide vancosamine-(1-2)-beta-D-glucopyranose


Type: oligosaccharide, Glycopeptide / Class: Antibiotic / Mass: 323.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: VANCOMYCIN IS A TRICYCLIC GLYCOPEPTIDE, GLYCOSYLATED BY A DISACCHARIDE (RESIDUES 8 AND 9) ON RESIDUE 4.
References: Vancomycin
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2122h-1b_1-5][ad621m-1a_1-5_3*C_3*N]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Glcp]{[(2+1)][a-L-2-deoxy-Fucp3N]{}}LINUCSPDB-CARE
#4: Chemical ChemComp-TYD / THYMIDINE-5'-DIPHOSPHATE


Mass: 402.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O11P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O
Compound detailsVANCOMYCIN IS A TRICYCLIC GLYCOPEPTIDE. THE SCAFFOLD IS A HEPTAPEPTIDE WITH THE CONFIGURATION D-D-L- ...VANCOMYCIN IS A TRICYCLIC GLYCOPEPTIDE. THE SCAFFOLD IS A HEPTAPEPTIDE WITH THE CONFIGURATION D-D-L-D-D-L-L. IT IS FURTHER GLYCOSYLATED BY A DISACCHARIDE MADE OF D-GLUCOSE AND VANCOSAMINE. HERE, VANCOMYCIN IS REPRESENTED BY GROUPING TOUGHER THE SEQUENCE (SEQRES) AND THE TWO LIGANDS (HET) BGC AND RER.
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: 3.98 Å3/Da / Density % sol: 69.1 %
Crystal growpH: 6.1
Details: NA,K PHOSPHATE, PH 6.1, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
Conc.: 1.3 M / Common name: sodium potassium phosphate / Details: pH6.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 2, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 36772 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Rsym value: 0.072 / Net I/σ(I): 12.6
Reflection shellResolution: 2.7→2.8 Å / Rsym value: 0.236 / % possible all: 98.3
Reflection
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 30 Å / Num. obs: 30058 / % possible obs: 98.3 % / Rmerge(I) obs: 0.072
Reflection shell
*PLUS
Rmerge(I) obs: 0.236

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Processing

Software
NameVersionClassification
SOLVEphasing
RESOLVEmodel building
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.8→30 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.269 1382 -RANDOM
Rwork0.221 ---
obs0.221 31440 93 %-
Displacement parametersBiso mean: 62.8 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å / Luzzati d res low obs: 5 Å
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5651 0 46 86 5783
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.37
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.04
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.274 / Rfactor Rwork: 0.228
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.04

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