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

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Basic information

Entry
Database: PDB / ID: 3otg
TitleCrystal Structure of CalG1, Calicheamicin Glycostyltransferase, TDP bound form
ComponentsCalG1
KeywordsTRANSFERASE / Calicheamicin / TDP / Structural Genomics / PSI-2 / Protein Structure Initiative / Center for Eukaryotic Structural Genomics / CESG / GT-B fold / Glycosyltransferase / 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
THYMIDINE-5'-DIPHOSPHATE / CalG1
Similarity search - Component
Biological speciesMicromonospora echinospora (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.08 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3147
Polymers43,7351
Non-polymers5796
Water5,639313
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: CalG1
hetero molecules

A: CalG1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,62814
Polymers87,4692
Non-polymers1,15912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
Buried area4520 Å2
ΔGint-109 kcal/mol
Surface area32570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.177, 106.177, 155.817
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein CalG1


Mass: 43734.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora echinospora (bacteria) / Gene: calG1, Q8KNF2 / 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.: 1 / Source method: obtained synthetically / Formula: C10H16N2O11P2
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 313 / 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: 2.9 Å3/Da / Density % sol: 57.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: Protein Solution (20mg/ml CalG1 protein, 20mM Tris pH 8) mixed in a 1:1 ratio with the well solution (20% PEG3350, 0.2M LiSO4, 100mM BisTris pH 6.5) Cryoprotected with 20% ethylene glycol, ...Details: Protein Solution (20mg/ml CalG1 protein, 20mM Tris pH 8) mixed in a 1:1 ratio with the well solution (20% PEG3350, 0.2M LiSO4, 100mM BisTris pH 6.5) Cryoprotected with 20% ethylene glycol, 20% PEG3350, 0.2M LiSO4, 100mM BisTris pH 6.5, 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: 23-ID-D / Wavelength: 0.9794, 0.9641
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 18, 2009 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Si(111) Double Crystal Monochromater / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.96411
ReflectionRedundancy: 41.9 % / Av σ(I) over netI: 62.35 / Number: 1281384 / Rmerge(I) obs: 0.082 / Χ2: 1.31 / D res high: 2.11 Å / D res low: 50 Å / Num. obs: 30569 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.725099.610.0422.16538
4.545.7299.910.0471.87441.4
3.974.5410010.0611.22342
3.613.9710010.0611.08342.4
3.353.6110010.0551.15442.7
3.153.3510010.0681.19342.8
2.993.1510010.0911.14143.1
2.862.9910010.1171.15943
2.752.8610010.1391.16143.2
2.662.7510010.1661.16843.3
2.582.6610010.1891.19343.2
2.52.5810010.2271.19143.3
2.442.510010.2791.22143.4
2.382.4410010.3511.25143.2
2.322.3810010.4111.29843.4
2.272.3210010.4681.33743.1
2.232.2710010.5811.44142.6
2.192.2310010.6531.26941.9
2.152.1910010.7661.34140.1
2.112.1599.710.8141.23932.7
ReflectionResolution: 2.08→50 Å / Num. obs: 31794 / % possible obs: 100 % / Redundancy: 41.9 % / Rmerge(I) obs: 0.082 / Χ2: 1.306 / Net I/σ(I): 12.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.11-2.1532.70.81414741.239199.7
2.15-2.1940.10.76614941.3411100
2.19-2.2341.90.65314911.2691100
2.23-2.2742.60.58115141.4411100
2.27-2.3243.10.46814911.3371100
2.32-2.3843.40.41114861.2981100
2.38-2.4443.20.35115181.2511100
2.44-2.543.40.27914921.2211100
2.5-2.5843.30.22715081.1911100
2.58-2.6643.20.18915231.1931100
2.66-2.7543.30.16614911.1681100
2.75-2.8643.20.13915261.1611100
2.86-2.99430.11715241.1591100
2.99-3.1543.10.09115221.1411100
3.15-3.3542.80.06815281.1931100
3.35-3.6142.70.05515421.1541100
3.61-3.9742.40.06115471.0831100
3.97-4.54420.06115721.2231100
4.54-5.7241.40.04716011.874199.9
5.72-50380.04217252.165199.6

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Phasing

PhasingMethod: MAD
Phasing MADD res high: 2.08 Å / D res low: 45.98 Å / FOM acentric: 0.505 / FOM centric: 0.29 / Reflection acentric: 27188 / Reflection centric: 4610
Phasing MAD set
IDR cullis acentricR cullis centricHighest resolution (Å)Lowest resolution (Å)Reflection acentricReflection centric
ISO_1002.0845.98259554477
ISO_20.8280.8052.0845.98258684468
ANO_10.58502.0845.98259520
ANO_20.80202.0845.98270890
Phasing MAD set shell
IDResolution (Å)R cullis acentricR cullis centricReflection acentricReflection centric
ISO_19.13-45.9800239218
ISO_16.52-9.1300496229
ISO_15.34-6.5200674226
ISO_14.63-5.3400812233
ISO_14.15-4.6300941233
ISO_13.79-4.15001036227
ISO_13.51-3.79001150233
ISO_13.28-3.51001240228
ISO_13.1-3.28001323233
ISO_12.94-3.1001406228
ISO_12.8-2.94001483229
ISO_12.68-2.8001561238
ISO_12.58-2.68001625236
ISO_12.49-2.58001696222
ISO_12.4-2.49001762239
ISO_12.32-2.4001816223
ISO_12.26-2.32001877238
ISO_12.19-2.26001924231
ISO_12.13-2.19002017232
ISO_12.08-2.1300877101
ANO_19.13-45.980.1502390
ANO_16.52-9.130.13204960
ANO_15.34-6.520.12706740
ANO_14.63-5.340.17908120
ANO_14.15-4.630.27209410
ANO_13.79-4.150.32010360
ANO_13.51-3.790.318011500
ANO_13.28-3.510.339012400
ANO_13.1-3.280.385013230
ANO_12.94-3.10.489014060
ANO_12.8-2.940.552014830
ANO_12.68-2.80.645015610
ANO_12.58-2.680.723016250
ANO_12.49-2.580.767016960
ANO_12.4-2.490.83017620
ANO_12.32-2.40.875018160
ANO_12.26-2.320.905018770
ANO_12.19-2.260.935019240
ANO_12.13-2.190.962020170
ANO_12.08-2.130.96808740
ISO_29.13-45.980.6560.652239217
ISO_26.52-9.130.6860.68496229
ISO_25.34-6.520.7330.684674226
ISO_24.63-5.340.7860.806812233
ISO_24.15-4.630.8290.865941233
ISO_23.79-4.150.8280.8591036227
ISO_23.51-3.790.8780.8561150233
ISO_23.28-3.510.8650.8431240228
ISO_23.1-3.280.8630.8741323233
ISO_22.94-3.10.8660.8321404227
ISO_22.8-2.940.8730.8521478228
ISO_22.68-2.80.8610.8731553238
ISO_22.58-2.680.8680.8611621236
ISO_22.49-2.580.8670.8721690222
ISO_22.4-2.490.8490.861754238
ISO_22.32-2.40.8440.8761809223
ISO_22.26-2.320.8420.8691864236
ISO_22.19-2.260.8170.821909230
ISO_22.13-2.190.8290.8912003230
ISO_22.08-2.130.9311.031872101
ANO_29.13-45.980.19202390
ANO_26.52-9.130.15304960
ANO_25.34-6.520.16106740
ANO_24.63-5.340.22608120
ANO_24.15-4.630.31309410
ANO_23.79-4.150.387010360
ANO_23.51-3.790.422011500
ANO_23.28-3.510.482012410
ANO_23.1-3.280.569013240
ANO_22.94-3.10.706014040
ANO_22.8-2.940.757014810
ANO_22.68-2.80.833015550
ANO_22.58-2.680.872016250
ANO_22.49-2.580.897016930
ANO_22.4-2.490.946017610
ANO_22.32-2.40.952018150
ANO_22.26-2.320.965018750
ANO_22.19-2.260.975019260
ANO_22.13-2.190.988020100
ANO_22.08-2.130.991020310
Phasing MAD shell
Resolution (Å)FOM acentricFOM centricReflection acentricReflection centric
9.13-45.980.8840.595239218
6.52-9.130.8440.566496229
5.34-6.520.850.547674226
4.63-5.340.7910.453812234
4.15-4.630.7330.375941234
3.79-4.150.70.351036227
3.51-3.790.6960.3061150234
3.28-3.510.6870.3371241229
3.1-3.280.6920.2771324233
2.94-3.10.6310.2991406229
2.8-2.940.6190.2741486229
2.68-2.80.5740.2341563238
2.58-2.680.5250.2281629236
2.49-2.580.4940.1921699223
2.4-2.490.440.1661769240
2.32-2.40.3910.1371822223
2.26-2.320.3370.1591888239
2.19-2.260.2880.1221941231
2.13-2.190.2440.1162024232
2.08-2.130.1590.0952048226

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
PHENIX1.6.1_357refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.08→45.976 Å / Occupancy max: 1 / Occupancy min: 0.41 / SU ML: 0.28 / σ(F): 1.33 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.227 1607 5.05 %
Rwork0.1926 --
obs0.1943 31794 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.984 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso max: 224.14 Å2 / Biso mean: 49.9016 Å2 / Biso min: 19.66 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.08→45.976 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2906 0 30 313 3249
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063086
X-RAY DIFFRACTIONf_angle_d1.0054220
X-RAY DIFFRACTIONf_chiral_restr0.062469
X-RAY DIFFRACTIONf_plane_restr0.005570
X-RAY DIFFRACTIONf_dihedral_angle_d13.9251131
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.08-2.14720.25361540.22322646280099
2.1472-2.22390.21921320.221727022834100
2.2239-2.3130.25281410.221326972838100
2.313-2.41820.24151370.212327202857100
2.4182-2.54570.24951430.207726882831100
2.5457-2.70520.26711420.207927202862100
2.7052-2.9140.26141530.21527162869100
2.914-3.20720.261440.208127462890100
3.2072-3.67110.22331470.187227652912100
3.6711-4.62450.15341540.150428122966100
4.6245-45.98720.22191600.17129753135100

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