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- PDB-1rrv: X-ray crystal structure of TDP-vancosaminyltransferase GtfD as a ... -

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Basic information

Entry
Database: PDB / ID: 1rrv
TitleX-ray crystal structure of TDP-vancosaminyltransferase GtfD as a complex with TDP and the natural substrate, desvancosaminyl vancomycin.
Components
  • DESVANCOSAMINYL VANCOMYCIN
  • GLYCOSYLTRANSFERASE GTFD
KeywordsTRANSFERASE/ANTIBIOTIC / GT-B / GLYCOSYLTRANSFERASE / ROSSMANN FOLD / GLYCOPEPTIDE / VACOSAMYCIN / ANTIBIOTIC / TRANSFERASE-ANTIBIOTIC COMPLEX
Function / homology
Function and homology information


devancosaminyl-vancomycin vancosaminetransferase / vancomycin biosynthetic process / hexosyltransferase activity / lipid glycosylation / carbohydrate metabolic process
Similarity search - Function
Glycosyltransferase family 28, N-terminal domain / Glycosyltransferase family 28 N-terminal domain / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DESVANCOSAMINYL VANCOMYCIN / beta-D-glucopyranose / : / THYMIDINE-5'-DIPHOSPHATE / : / Devancosaminyl-vancomycin vancosaminetransferase
Similarity search - Component
Biological speciesAMYCOLATOPSIS ORIENTALIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMulichak, A.M. / Lu, W. / Losey, H.C. / Walsh, C.T. / Garavito, R.M.
CitationJournal: Biochemistry / Year: 2004
Title: Crystal Structure of Vancosaminyltransferase Gtfd from the Vancomycin Biosynthetic Pathway: Interactions with Acceptor and Nucleotide Ligands
Authors: Mulichak, A.M. / Lu, W. / Losey, H.C. / Walsh, C.T. / Garavito, R.M.
History
DepositionDec 9, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2004Provider: 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 1.5Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.6Nov 1, 2017Group: Derived calculations / Category: pdbx_struct_assembly / Item: _pdbx_struct_assembly.method_details
Revision 2.0Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence / Structure summary
Category: chem_comp / entity ...chem_comp / entity / entity_poly / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 / _struct_conn_type.id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 23, 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 2.2Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _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 GTFD
B: GLYCOSYLTRANSFERASE GTFD
C: DESVANCOSAMINYL VANCOMYCIN
D: DESVANCOSAMINYL VANCOMYCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,63113
Polymers90,1124
Non-polymers1,5199
Water9,008500
1
A: GLYCOSYLTRANSFERASE GTFD
C: DESVANCOSAMINYL VANCOMYCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8617
Polymers45,0562
Non-polymers8065
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-33.2 kcal/mol
Surface area15750 Å2
MethodPISA
2
B: GLYCOSYLTRANSFERASE GTFD
D: DESVANCOSAMINYL VANCOMYCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7696
Polymers45,0562
Non-polymers7144
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-31 kcal/mol
Surface area15400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.670, 64.120, 144.080
Angle α, β, γ (deg.)90.00, 91.73, 90.00
Int Tables number4
Space group name H-MP1211
DetailsBiological assembly is a monomer.

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Components

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Protein / Protein/peptide / Sugars , 3 types, 6 molecules ABCD

#1: Protein GLYCOSYLTRANSFERASE GTFD


Mass: 43905.879 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AMYCOLATOPSIS ORIENTALIS (bacteria) / Gene: GTFD / Plasmid: PET22B / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9AFC7
#2: Protein/peptide DESVANCOSAMINYL VANCOMYCIN


Type: Glycopeptide / Class: Antibiotic / Mass: 1149.977 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: DESVANCOSAMINYL VANCOMYCIN IS AN INTERMIDIATE IN VANCOMYCIN BIOSYNTHESIS. IT IS TRICYCLIC GLYCOPEPTIDE, GLYCOSYLATED BY D-GLUCOSE (RESIDUE 8) ON RESIDUE 4.
Source: (natural) AMYCOLATOPSIS ORIENTALIS (bacteria) / References: NOR: NOR00681, DESVANCOSAMINYL VANCOMYCIN
#6: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, beta linking, Glycopeptide / Class: Antibiotic / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
Details: DESVANCOSAMINYL VANCOMYCIN IS AN INTERMIDIATE IN VANCOMYCIN BIOSYNTHESIS. IT IS TRICYCLIC GLYCOPEPTIDE, GLYCOSYLATED BY D-GLUCOSE (RESIDUE 8) ON RESIDUE 4.
References: DESVANCOSAMINYL VANCOMYCIN
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 507 molecules

#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-TYD / THYMIDINE-5'-DIPHOSPHATE / Thymidine diphosphate


Mass: 402.188 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N2O11P2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 500 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsVANCOMYCIN DESVANCOSAMINYL IS A TRICYCLIC GLYCOPEPTIDE, A MEMBER OF THE VANCOMYCIN FAMILY. THE ...VANCOMYCIN DESVANCOSAMINYL IS A TRICYCLIC GLYCOPEPTIDE, A MEMBER OF THE VANCOMYCIN FAMILY. THE SCAFFOLD IS A HEPTAPEPTIDE WITH THE CONFIGURATION D-D-L-D-D-L-L. IT IS FURTHER GLYCOSYLATED BY A D-GLUCOSE HERE, DESVANCOSAMINYL ANCOMYCIN IS REPRESENTED BY GROUPING TOGETHER THE SEQUENCE (SEQRES) AND THE LIGAND (HET) BGC.

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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: 2.66 Å3/Da / Density % sol: 53.79 %
Crystal growpH: 7
Details: NA,K PHOSPHATE, PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K

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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: Jul 17, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.96→30 Å / Num. obs: 66022 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Rsym value: 0.074 / Net I/σ(I): 11.4
Reflection shellResolution: 1.96→2.04 Å / % possible all: 95.9

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
MAR345data collection
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PN3

1pn3


Resolution: 2→30 Å / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflectionSelection details
Rfree0.252 2668 RANDOM
Rwork0.21 --
obs0.21 55329 -
Displacement parametersBiso mean: 37.9 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5975 0 92 500 6567
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.27
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1
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

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