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- PDB-3oti: Crystal Structure of CalG3, Calicheamicin Glycostyltransferase, T... -

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Basic information

Entry
Database: PDB / ID: 3oti
TitleCrystal Structure of CalG3, Calicheamicin Glycostyltransferase, TDP and calicheamicin T0 bound form
ComponentsCalG3
Keywordstransferase/antibiotic / Calicheamicin / TDP / Structural Genomics / PSI-2 / Protein Structure Initiative / Center for Eukaryotic Structural Genomics / CESG / GT-B fold / Glycosyltransferase / transferase-antibiotic complex / Enzyme Discovery for Natural Product Biosynthesis / NatPro
Function / homology
Function and homology information


UDP-glycosyltransferase activity / glucosyltransferase activity / antibiotic biosynthetic process
Similarity search - Function
: / Erythromycin biosynthesis protein CIII-like, 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
Calicheamicin T0 / THYMIDINE-5'-DIPHOSPHATE / CalG3
Similarity search - Component
Biological speciesMicromonospora echinospora (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.597 Å
AuthorsChang, A. / Singh, S. / Bingman, C.A. / Thorson, J.S. / Phillips Jr., G.N. / Center for Eukaryotic Structural Genomics (CESG) / Enzyme Discovery for Natural Product Biosynthesis (NatPro)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Complete set of glycosyltransferase structures in the calicheamicin biosynthetic pathway reveals the origin of regiospecificity.
Authors: Chang, A. / Singh, S. / Helmich, K.E. / Goff, R.D. / Bingman, C.A. / Thorson, J.S. / Phillips, G.N.
History
DepositionSep 11, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 2, 2011Group: Database references
Revision 1.3Aug 8, 2012Group: Structure summary
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: CalG3
B: CalG3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,0708
Polymers86,0262
Non-polymers2,0456
Water16,952941
1
A: CalG3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0354
Polymers43,0131
Non-polymers1,0223
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CalG3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0354
Polymers43,0131
Non-polymers1,0223
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5250 Å2
ΔGint-71 kcal/mol
Surface area27780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.567, 135.090, 62.093
Angle α, β, γ (deg.)90.000, 95.750, 90.000
Int Tables number4
Space group name H-MP1211
DetailsThe biological unit is a monomer.

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Components

#1: Protein CalG3


Mass: 43012.824 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora echinospora (bacteria) / Gene: calG3 / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8KND7
#2: Chemical ChemComp-TYD / THYMIDINE-5'-DIPHOSPHATE / Thymidine diphosphate


Mass: 402.188 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N2O11P2
#3: Chemical ChemComp-C0T / Calicheamicin T0 / methyl {(1R,4Z,8S,13E)-8-{[4,6-dideoxy-4-(hydroxyamino)-beta-D-glucopyranosyl]oxy}-1-hydroxy-13-[2-(methyltrisulfanyl)ethylidene]-11-oxobicyclo[7.3.1]trideca-4,9-diene-2,6-diyn-10-yl}carbamate


Mass: 584.682 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H28N2O9S3
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 941 / 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: 2.21 Å3/Da / Density % sol: 44.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: Protein Solution (10mg/ml CalG3 protein, 10mM Tris pH 7.5, 50mM NaCl, 25mM TDP, calicheamicin T0) mixed in a 1:1 ratio with the well solution (28% MEPEG2K, 160mM Na3Citrate, 100mM NaAcetate ...Details: Protein Solution (10mg/ml CalG3 protein, 10mM Tris pH 7.5, 50mM NaCl, 25mM TDP, calicheamicin T0) mixed in a 1:1 ratio with the well solution (28% MEPEG2K, 160mM Na3Citrate, 100mM NaAcetate pH 4.5) Cryoprotected with 20% Ethylene Glycol, 28% MEPEG2K, 160mM Na3Citrate, 100mM NaAcetate pH 4.5, vapor diffusion, hanging drop, temperature 298K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9794 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 20, 2010 / Details: mirrors and beryllium lenses
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.597→50 Å / Num. obs: 96516 / % possible obs: 98 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.095 / Χ2: 1.018 / Net I/σ(I): 10.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.6-1.634.60.38841830.852184.8
1.63-1.665.20.35843910.874190.1
1.66-1.695.60.33746010.868192.7
1.69-1.726.10.32546530.919195.3
1.72-1.766.40.29248260.929198.3
1.76-1.86.80.26548730.987199.6
1.8-1.857.10.24649121.0091100
1.85-1.97.40.21649511.031100
1.9-1.957.60.19448741.0651100
1.95-2.027.60.16849291.0021100
2.02-2.097.70.14749340.9551100
2.09-2.177.70.13349271.0861100
2.17-2.277.70.11548890.9841100
2.27-2.397.70.10349331.1231100
2.39-2.547.70.09349181.0481100
2.54-2.747.80.0949081.1081100
2.74-3.017.80.08649501.1011100
3.01-3.457.80.07449221.1381100
3.45-4.347.70.06849501.1091100
4.34-507.50.06549920.911199.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å29.23 Å
Translation2.5 Å29.23 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.2.4phasing
PHENIX1.6.1_357refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXPHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.597→29.234 Å / Occupancy max: 1 / Occupancy min: 0.32 / SU ML: 0.17 / σ(F): 0.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1806 1948 2.09 %
Rwork0.1522 --
obs0.1528 93367 94.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.437 Å2 / ksol: 0.378 e/Å3
Displacement parametersBiso max: 86.75 Å2 / Biso mean: 18.584 Å2 / Biso min: 5.35 Å2
Baniso -1Baniso -2Baniso -3
1-3.2406 Å2-0 Å21.1844 Å2
2---2.1103 Å20 Å2
3----1.4631 Å2
Refinement stepCycle: LAST / Resolution: 1.597→29.234 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5750 0 128 941 6819
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0136141
X-RAY DIFFRACTIONf_angle_d1.5578424
X-RAY DIFFRACTIONf_chiral_restr0.1973
X-RAY DIFFRACTIONf_plane_restr0.0071106
X-RAY DIFFRACTIONf_dihedral_angle_d20.3852268
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5972-1.63710.24941180.19265237535576
1.6371-1.68140.22181210.17795780590184
1.6814-1.73090.23041310.17026098622989
1.7309-1.78670.21261340.17086377651193
1.7867-1.85060.1831380.16336529666795
1.8506-1.92460.2071450.15626675682097
1.9246-2.01220.18381430.15546676681997
2.0122-2.11830.20141440.14916766691098
2.1183-2.25090.17351440.14976814695899
2.2509-2.42470.20711460.15496824697099
2.4247-2.66850.19631450.15568747019100
2.6685-3.05430.1751450.149668947039100
3.0543-3.84670.15591470.136169307077100
3.8467-29.23860.13491470.135269457092100

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