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- PDB-3ia7: Crystal Structure of CalG4, the Calicheamicin Glycosyltransferase -

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Basic information

Entry
Database: PDB / ID: 3ia7
TitleCrystal Structure of CalG4, the Calicheamicin Glycosyltransferase
ComponentsCalG4
KeywordsTRANSFERASE / Glycosysltransferase / Calicheamicin / CalG4 / enediyne
Function / homology
Function and homology information


antibiotic metabolic process / UDP-glycosyltransferase activity / hexosyltransferase activity / metal ion binding
Similarity search - Function
UDP-glycosyltransferase, MGT-like / 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
Biological speciesMicromonospora echinospora (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.91 Å
AuthorsChang, A. / Singh, S. / Bingman, C.A. / Thorson, J.S. / Phillips Jr., G.N.
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
DepositionJul 13, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 2, 2011Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CalG4
B: CalG4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,9655
Polymers88,8502
Non-polymers1163
Water7,873437
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-50 kcal/mol
Surface area32860 Å2
MethodPISA
2
A: CalG4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5003
Polymers44,4251
Non-polymers762
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: CalG4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4652
Polymers44,4251
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.749, 66.966, 86.616
Angle α, β, γ (deg.)90.000, 93.530, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CalG4


Mass: 44424.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora echinospora (bacteria) / Strain: Micromonospora echinospora / Gene: calG4, Q8KNC3 / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): B834 P(RARE2) / References: UniProt: Q8KNC3
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 437 / 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: 2.76 Å3/Da / Density % sol: 55.45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: Protein Solution (10 mg/ml CalG4 Protein, 0.05 M NaCl, 0.005 M Tris pH 8) mixed in a 1:1 ratio with the Well Solution (19% PEG4K, 0.08 M CaCl2, 0.1 M CHES pH 9.5) Cryoprotected with 25% ...Details: Protein Solution (10 mg/ml CalG4 Protein, 0.05 M NaCl, 0.005 M Tris pH 8) mixed in a 1:1 ratio with the Well Solution (19% PEG4K, 0.08 M CaCl2, 0.1 M CHES pH 9.5) Cryoprotected with 25% ethylene glycol, 19% PEG4K, 0.08 M CaCl2, 0.1 M CHES pH 9.5, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97945, 0.96421
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 31, 2008 / 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
10.979451
20.964211
ReflectionRedundancy: 7.2 % / Av σ(I) over netI: 21.83 / Number: 537130 / Rmerge(I) obs: 0.074 / Χ2: 1.04 / D res high: 1.91 Å / D res low: 50 Å / Num. obs: 74332 / % possible obs: 98.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.115099.910.0490.9127.6
3.274.1110010.061.0287.7
2.853.2710010.0681.0597.7
2.592.8510010.0971.0367.7
2.412.5910010.1231.0737.7
2.262.4110010.1511.0477.7
2.152.2610010.2061.0257.7
2.062.1510010.2941.0687.4
1.982.0699.410.371.0646.3
1.911.9884.610.4511.084.4
ReflectionResolution: 1.91→50 Å / Num. obs: 74332 / % possible obs: 98.4 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.074 / Χ2: 1.036 / Net I/σ(I): 11.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.91-1.984.40.45163581.08184.6
1.98-2.066.30.3774701.064199.4
2.06-2.157.40.29475021.0681100
2.15-2.267.70.20674931.0251100
2.26-2.417.70.15175521.0471100
2.41-2.597.70.12375041.0731100
2.59-2.857.70.09775511.0361100
2.85-3.277.70.06875781.0591100
3.27-4.117.70.0675811.0281100
4.11-507.60.04977430.912199.9

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Phasing

PhasingMethod: MAD
Phasing MAD set
IDHighest resolution (Å)Lowest resolution (Å)Power acentricPower centricReflection acentricReflection centric
ISO_11.9145.6600711263134
ISO_21.9145.660.7510.664626182869
ANO_11.9145.661.0230696960
ANO_21.9145.660.620622320
Phasing MAD set shell
IDResolution (Å)Power acentricPower centricReflection acentricReflection centric
ISO_18.41-45.6600768154
ISO_16-8.41001450159
ISO_14.91-6001884157
ISO_14.26-4.91002230157
ISO_13.81-4.26002535157
ISO_13.48-3.81002810153
ISO_13.23-3.48003062164
ISO_13.02-3.23003287154
ISO_12.85-3.02003537159
ISO_12.7-2.85003692157
ISO_12.58-2.7003902152
ISO_12.47-2.58004107162
ISO_12.37-2.47004265157
ISO_12.28-2.37004456155
ISO_12.21-2.28004625162
ISO_12.14-2.21004739149
ISO_12.07-2.14004894159
ISO_12.02-2.07005065151
ISO_11.96-2.02005119164
ISO_11.91-1.96004699152
ANO_18.41-45.661.76907670
ANO_16-8.412.35014500
ANO_14.91-62.206018840
ANO_14.26-4.911.744022300
ANO_13.81-4.261.618025350
ANO_13.48-3.811.631028100
ANO_13.23-3.481.623030610
ANO_13.02-3.231.587032870
ANO_12.85-3.021.463035370
ANO_12.7-2.851.217036920
ANO_12.58-2.71.078039020
ANO_12.47-2.580.921041070
ANO_12.37-2.470.805042650
ANO_12.28-2.370.674044560
ANO_12.21-2.280.556046250
ANO_12.14-2.210.459047390
ANO_12.07-2.140.389048860
ANO_12.02-2.070.33049530
ANO_11.96-2.020.287047110
ANO_11.91-1.960.258037990
ISO_28.41-45.661.9341.419768152
ISO_26-8.411.8751.3171450159
ISO_24.91-61.4921.0711884157
ISO_24.26-4.911.1150.7252230156
ISO_23.81-4.260.9490.6742535157
ISO_23.48-3.810.8750.5732810153
ISO_23.23-3.480.8780.5523062164
ISO_23.02-3.230.8890.583286154
ISO_22.85-3.020.860.5573534159
ISO_22.7-2.850.8220.6113691156
ISO_22.58-2.70.7430.4763901152
ISO_22.47-2.580.6530.4184105162
ISO_22.37-2.470.5630.3884260157
ISO_22.28-2.370.4780.3214450155
ISO_22.21-2.280.4040.3224620162
ISO_22.14-2.210.3370.2524734149
ISO_22.07-2.140.2750.2044888159
ISO_22.02-2.070.2270.1754969151
ISO_21.96-2.020.1970.18144155
ISO_21.91-1.960000
ANO_28.41-45.661.56607670
ANO_26-8.412.188014500
ANO_24.91-62.051018840
ANO_24.26-4.911.664022300
ANO_23.81-4.261.409025350
ANO_23.48-3.811.294028100
ANO_23.23-3.481.193030620
ANO_23.02-3.231.022032860
ANO_22.85-3.020.887035340
ANO_22.7-2.850.71036910
ANO_22.58-2.70.582039000
ANO_22.47-2.580.472041050
ANO_22.37-2.470.389042600
ANO_22.28-2.370.322044500
ANO_22.21-2.280.261046200
ANO_22.14-2.210.224047330
ANO_22.07-2.140.183048580
ANO_22.02-2.070.172047370
ANO_21.96-2.020.16013200
ANO_21.91-1.960000
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
137.28910.98247.389SE28.471.18
257.81525.27479.526SE32.291.34
337.564-0.31425.073SE30.891.39
463.180.02772.856SE32.251.36
535.31118.49524.259SE60.641.05
631.68823.48144.008SE36.010.62
7-42.529-22.262-77.553SE20.30.14
8-57.826-10.882-52.105SE56.140.13
9-40.958-10.788-55.442SE36.010.09
10-37.551-0.609-59.159SE50.610.09
11-21.167-11.049-42.145SE54.340.27
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 74260
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
10.36-10057.70.847508
7.33-10.3648.10.942890
5.98-7.3350.60.9411150
5.18-5.9846.20.9411341
4.63-5.1851.20.951535
4.23-4.6353.70.951669
3.92-4.2350.30.9521818
3.66-3.9253.40.941954
3.45-3.6654.60.942061
3.28-3.4554.30.9262202
3.12-3.28550.922288
2.99-3.1254.20.9122395
2.87-2.9955.70.9132506
2.77-2.8757.10.9132594
2.68-2.7758.50.9092696
2.59-2.6861.40.9052791
2.51-2.5961.50.92849
2.44-2.51630.8972945
2.38-2.4465.50.93036
2.32-2.3867.60.9013105
2.26-2.3270.20.9033191
2.21-2.2672.20.9083257
2.16-2.2173.90.8973327
2.12-2.1676.90.9023383
2.07-2.1277.60.8933488
2.03-2.0780.70.8913545
1.99-2.0382.60.893592
1.96-1.9982.50.8483565
1.91-1.9683.90.7944579

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
DM5phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 1.91→45.64 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.882 / WRfactor Rfree: 0.318 / WRfactor Rwork: 0.266 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.797 / SU R Cruickshank DPI: 0.191 / SU Rfree: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.191 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.301 3745 5 %RANDOM
Rwork0.253 ---
obs0.256 74257 98.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 63.6 Å2 / Biso mean: 21.459 Å2 / Biso min: 5.01 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20.04 Å2
2--0.07 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.91→45.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6090 0 3 437 6530
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0226340
X-RAY DIFFRACTIONr_angle_refined_deg1.5671.9518665
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9015791
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.11422.706303
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.35715932
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0461558
X-RAY DIFFRACTIONr_chiral_restr0.1110.2949
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215011
X-RAY DIFFRACTIONr_mcbond_it0.9471.53953
X-RAY DIFFRACTIONr_mcangle_it1.56526370
X-RAY DIFFRACTIONr_scbond_it2.42332387
X-RAY DIFFRACTIONr_scangle_it3.6434.52295
LS refinement shellResolution: 1.912→1.962 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 268 -
Rwork0.315 4615 -
all-4883 -
obs--88.52 %

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