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- PDB-3h4i: Chimeric Glycosyltransferase for the generation of novel natural ... -

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Basic information

Entry
Database: PDB / ID: 3h4i
TitleChimeric Glycosyltransferase for the generation of novel natural products
ComponentsGlycosyltransferase GtfA, Glycosyltransferase
KeywordsTRANSFERASE / glycosyltransferase / GtfA / chimeric protein / vancomycin / teicoplanin / antibiotic
Function / homology
Function and homology information


chloroorienticin B synthase / vancomycin biosynthetic process / UDP-glycosyltransferase activity / hexosyltransferase activity / lipid glycosylation / acyltransferase activity / ligase activity / carbohydrate metabolic process / nucleotide binding
Similarity search - Function
Glycosyltransferase family 28, N-terminal domain / Glycosyltransferase family 28 N-terminal domain / Glycosyltransferase family 28 C-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
Chem-U2F / dTDP-epi-vancosaminyltransferase / Chloroorienticin B synthase/vancomycin aglycone glucosyltransferase
Similarity search - Component
Biological speciesAmycolatopsis orientalis (bacteria)
Actinoplanes teichomyceticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsDias, M.V.B. / Truman, A.W. / Wu, S. / Blundell, T.L. / Huang, F. / Spencer, J.B.
CitationJournal: Chem.Biol. / Year: 2009
Title: Chimeric glycosyltransferases for the generation of hybrid glycopeptides
Authors: Truman, A.W. / Dias, M.V.B. / Wu, S. / Blundell, T.L. / Huang, F. / Spencer, J.B.
History
DepositionApr 20, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 9, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _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 GtfA, Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8684
Polymers42,1081
Non-polymers7603
Water11,349630
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.480, 129.830, 67.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-851-

HOH

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Components

#1: Protein Glycosyltransferase GtfA, Glycosyltransferase / GtfA / orf1 / PCZA361.19 / GtfA protein


Mass: 42107.586 Da / Num. of mol.: 1 / Fragment: UNP residues 1-214, UNP residues 218-393
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amycolatopsis orientalis (bacteria), (gene. exp.) Actinoplanes teichomyceticus (bacteria)
Gene: GtfA / Plasmid: pET 28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P96558, UniProt: Q6ZZJ7, Transferases; Glycosyltransferases
#2: Chemical ChemComp-U2F / URIDINE-5'-DIPHOSPHATE-2-DEOXY-2-FLUORO-ALPHA-D-GLUCOSE


Mass: 568.293 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23FN2O16P2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 630 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHERE ARE CONFLICTS BETWEEN THE REPORTED SEQUENCE AND DATABASE REFERENCE ONE(P96558 IN UNIPROT). ...THERE ARE CONFLICTS BETWEEN THE REPORTED SEQUENCE AND DATABASE REFERENCE ONE(P96558 IN UNIPROT). ACCORDING TO THE DEPOSITORS, THE DIFFERENCE IN THE RESIDUES IS POSSIBLY DUE TO DIFFERENT ANNOTATION IN THE DATA BASE OR DUE TO THE CONSTRUCTION OF THE CHIMERIC PROTEIN. THIS COORDINATES USE NON-SEQUENTIAL RESIDUE NUMBERING FOR CLARIFICATION OF THE EXPRESSION TAGS AT THE C-TERMINUS.

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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: 2.9 Å3/Da / Density % sol: 57.55 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris-HCL, 1.2-2M ammonium sulphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.98 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Dec 5, 2007
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.3→29.92 Å / Num. obs: 119259 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7 % / Rmerge(I) obs: 0.074 / Num. measured all: 838486
Reflection shellResolution: 1.3→1.37 Å / Redundancy: 7 % / Rmerge(I) obs: 0.569 / Num. unique all: 17244 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PN3

1pn3


Resolution: 1.3→29.25 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.311 / SU ML: 0.026 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.045 / ESU R Free: 0.043 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18383 5975 5 %RANDOM
Rwork0.16382 ---
all0.17 143104 --
obs0.16481 113256 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.492 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.3→29.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2862 0 46 630 3538
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222969
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2221.9924073
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1495390
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.45522.566113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.10515414
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0211528
X-RAY DIFFRACTIONr_chiral_restr0.0730.2474
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022278
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.190.21521
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.22075
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1060.2479
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1410.256
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1280.246
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6841.51993
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.08323122
X-RAY DIFFRACTIONr_scbond_it2.65331087
X-RAY DIFFRACTIONr_scangle_it2.594.5951
X-RAY DIFFRACTIONr_rigid_bond_restr2.53233080
X-RAY DIFFRACTIONr_sphericity_free2.0973630
X-RAY DIFFRACTIONr_sphericity_bonded1.89832908
LS refinement shellResolution: 1.302→1.336 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 452 -
Rwork0.237 8263 -
obs--99.99 %

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