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- PDB-1iir: Crystal Structure of UDP-glucosyltransferase GtfB -

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Basic information

Entry
Database: PDB / ID: 1iir
TitleCrystal Structure of UDP-glucosyltransferase GtfB
Componentsglycosyltransferase GtfB
KeywordsTRANSFERASE / glycosyltransferase / rossmann fold
Function / homology
Function and homology information


vancomycin aglycone glucosyltransferase / 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 aglycone glucosyltransferase
Similarity search - Component
Biological speciesAmycolatopsis orientalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.8 Å
AuthorsMulichak, A.M. / Losey, H.C. / Walsh, C.T. / Garavito, R.M.
CitationJournal: Structure / Year: 2001
Title: Structure of the UDP-glucosyltransferase GtfB that modifies the heptapeptide aglycone in the biosynthesis of vancomycin group antibiotics.
Authors: Mulichak, A.M. / Losey, H.C. / Walsh, C.T. / Garavito, R.M.
History
DepositionApr 24, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: glycosyltransferase GtfB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9224
Polymers43,7771
Non-polymers1453
Water5,278293
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.110, 102.110, 83.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-1404-

MG

21A-1579-

HOH

31A-1619-

HOH

41A-1656-

HOH

51A-1689-

HOH

61A-1692-

HOH

DetailsEnzyme is a monomer.

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Components

#1: Protein glycosyltransferase GtfB / UDP-GLYCOSYLTRANSFERASE GTFB


Mass: 43777.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amycolatopsis orientalis (bacteria) / Strain: A82846 / Plasmid: pET22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P96559, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / Source method: isolated from a natural source / Formula: H2O

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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: 2.48 Å3/Da / Density % sol: 50.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: magnesium sulfate, PEG 400, MES buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
21.53 M1reservoirMgSO4
32 %PEG4001reservoir
4100 mMMES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.033 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Jun 8, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 41142 / Num. obs: 41091 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 18.8 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 26.8
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 6 % / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 5 / Num. unique all: 4040 / % possible all: 100

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS0.9refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 1.8→30 Å / σ(F): 1 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Missing residues 56-62, 140-148, 246-248, 402-415 are disordered and unobserved in crystal structure. Also, for some residues side chain atoms are disordered and omitted from refined ...Details: Missing residues 56-62, 140-148, 246-248, 402-415 are disordered and unobserved in crystal structure. Also, for some residues side chain atoms are disordered and omitted from refined coordinates (C8, R11, E41, R63, E92, I149, D150, Q160, R273, D282, D283).
RfactorNum. reflection% reflectionSelection details
Rfree0.231 2867 7.2 %RANDOM
Rwork0.211 ---
all-41357 --
obs-40013 --
Refine analyzeLuzzati coordinate error obs: 0.22 Å / Luzzati sigma a obs: 0.13 Å
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2792 0 7 293 3092
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21
X-RAY DIFFRACTIONc_improper_angle_d0.9
LS refinement shellResolution: 1.8→1.86 Å
RfactorNum. reflection% reflection
Rfree0.294 198 -
Rwork0.241 --
obs-3742 92 %
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 30 Å / σ(F): 1 / % reflection Rfree: 7.2 % / Rfactor obs: 0.211
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.9
LS refinement shell
*PLUS
Rfactor Rfree: 0.294 / Rfactor Rwork: 0.241

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