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- PDB-3oth: Crystal Structure of CalG1, Calicheamicin Glycostyltransferase, T... -

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Basic information

Entry
Database: PDB / ID: 3oth
TitleCrystal Structure of CalG1, Calicheamicin Glycostyltransferase, TDP and calicheamicin alpha3I bound form
ComponentsCalG1
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


vancomycin biosynthetic process / UDP-glycosyltransferase activity / hexosyltransferase activity / lipid glycosylation / carbohydrate metabolic process
Similarity search - Function
Glycosyltransferase family 28, N-terminal domain / Glycosyltransferase family 28 N-terminal domain / UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Calicheamicin alpha3I / THYMIDINE-5'-DIPHOSPHATE / CalG1
Similarity search - Component
Biological speciesMicromonospora echinospora (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.301 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CalG1
B: CalG1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,6966
Polymers87,4692
Non-polymers3,2274
Water7,152397
1
A: CalG1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3483
Polymers43,7351
Non-polymers1,6132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CalG1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3483
Polymers43,7351
Non-polymers1,6132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.809, 100.100, 169.881
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsThe biological unit is a monomer.

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Components

#1: Protein CalG1


Mass: 43734.711 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora echinospora (bacteria) / Gene: calG1 / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): B834 P(RARE2) / References: UniProt: Q8KNF2
#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-CLJ / Calicheamicin alpha3I / S-[(2R,3S,4S,6S)-6-[[(2R,3S,4S,5R,6R)-4,5-dihydroxy-6-[[(2S,5Z,9R,13E)-9-hydroxy-12-(methoxycarbonylamino)-13-(2-methylsulfanyldisulfanylethylidene)-11-oxo-2-bicyclo[7.3.1]trideca-1(12),5-dien-3,7-diynyl]oxy]-2-methyl-oxan-3-yl]amino]oxy-4-hydroxy-2-methyl-oxan-3-yl] 4-[(2S,3R,4R,5S,6S)-3,5-dihydroxy-4-methoxy-6-methyl-oxan-2-yl]oxy-5-iodo-2,3-dimethoxy-6-methyl-benzenecarbothioate


Mass: 1211.138 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C47H59IN2O19S4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 397 / 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: 2.23 Å3/Da / Density % sol: 44.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Protein Solution (20mg/ml CalG1 protein, 20mM Tris pH 8, 25mM TDP) mixed in a 1:1 ratio with the well solution (16% MEPEG5K, 160mM CaCl2, 100mM MES/Acetate pH 5.5) Cryoprotected with 20% ...Details: Protein Solution (20mg/ml CalG1 protein, 20mM Tris pH 8, 25mM TDP) mixed in a 1:1 ratio with the well solution (16% MEPEG5K, 160mM CaCl2, 100mM MES/Acetate pH 5.5) Cryoprotected with 20% Glycerol, 24% MEPEG5K, 160mM CaCl2, 100mM MES/Acetate pH 5.5, 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: Jul 9, 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: 2.3→50 Å / Num. obs: 34067 / % possible obs: 95.9 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.126 / Χ2: 1.033 / Net I/σ(I): 6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.344.60.31312810.698174.7
2.34-2.384.80.3113911.044179.3
2.38-2.435.10.3314951.072185.6
2.43-2.485.40.30415320.786189.4
2.48-2.535.80.2916920.779195.2
2.53-2.596.20.29316760.797197
2.59-2.666.40.26717310.818198.2
2.66-2.736.70.23217240.941198.5
2.73-2.816.90.22317450.959199.5
2.81-2.970.20817480.956199.5
2.9-37.10.1817391.083199.7
3-3.127.10.15117701.0611100
3.12-3.267.20.13217871.2641100
3.26-3.447.20.1117611.1871100
3.44-3.657.20.117781.0591100
3.65-3.937.30.09717921.1621100
3.93-4.337.30.0817881.0461100
4.33-4.957.30.07918231.1071100
4.95-6.247.20.08618421.0981100
6.24-506.60.08919721.303199.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
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: 2.301→43.121 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.29 / σ(F): 0.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2466 1930 5.83 %
Rwork0.1937 --
obs0.1968 33078 92.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 82.41 Å2 / Biso mean: 20.7078 Å2 / Biso min: 1.49 Å2
Baniso -1Baniso -2Baniso -3
1--4.294 Å20 Å2-0 Å2
2--6.7405 Å20 Å2
3----1.9259 Å2
Refinement stepCycle: LAST / Resolution: 2.301→43.121 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5818 0 174 397 6389
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056166
X-RAY DIFFRACTIONf_angle_d0.9558437
X-RAY DIFFRACTIONf_chiral_restr0.059952
X-RAY DIFFRACTIONf_plane_restr0.0031117
X-RAY DIFFRACTIONf_dihedral_angle_d222289
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 (%)
2.3014-2.3590.256970.20551589168668
2.359-2.42270.30861120.21931820193277
2.4227-2.4940.2741260.21721966209284
2.494-2.57450.28281330.21492153228691
2.5745-2.66650.24671370.21192223236094
2.6665-2.77330.26731390.20522253239296
2.7733-2.89950.26921420.21762318246097
2.8995-3.05230.29151460.21152333247998
3.0523-3.24350.2721410.19932337247898
3.2435-3.49380.23651490.18652353250299
3.4938-3.84520.23431490.17512392254199
3.8452-4.40110.22121480.157624132561100
4.4011-5.54310.1951530.160924432596100
5.5431-43.12850.19821580.18842555271399

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