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- PDB-3tos: Crystal Structure of CalS11, Calicheamicin Methyltransferase -

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Basic information

Entry
Database: PDB / ID: 3tos
TitleCrystal Structure of CalS11, Calicheamicin Methyltransferase
ComponentsCalS11
KeywordsTRANSFERASE / Methyltransferase / Calicheamicin / CalS11 / Structural genomics / Protein Structure Initiative / PSI / NatPro / Enzyme Discovery for Natural Product Biosynthesis / Center for Eukaryotic Structural Genomics / CESG
Function / homology
Function and homology information


O-methyltransferase activity
Similarity search - Function
Methyltransferase domain / Macrocin-O-methyltransferase / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GLUTAMIC ACID / S-ADENOSYL-L-HOMOCYSTEINE / CalS11
Similarity search - Component
Biological speciesMicromonospora echinospora (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsChang, A. / Aceti, D.J. / Beebe, E.T. / Makino, S.-I. / Wrobel, R.L. / Bingman, C.A. / Thorson, J.S. / Phillips Jr., G.N. / Center for Eukaryotic Structural Genomics (CESG) / Enzyme Discovery for Natural Product Biosynthesis (NatPro)
CitationJournal: To be Published
Title: Crystal Structure of CalS11, Calicheamicin methyltransferase
Authors: Chang, A. / Aceti, D.J. / Beebe, E.T. / Makino, S.-I. / Wrobel, R.L. / Bingman, C.A. / Thorson, J.S. / Phillips Jr., G.N.
History
DepositionSep 6, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2012Group: Structure summary
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CalS11
B: CalS11
C: CalS11
D: CalS11
E: CalS11
F: CalS11
G: CalS11
H: CalS11
I: CalS11
J: CalS11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)297,41955
Polymers290,94310
Non-polymers6,47645
Water93,7145202
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area60790 Å2
ΔGint-442 kcal/mol
Surface area73580 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15620 Å2
ΔGint-97 kcal/mol
Surface area50960 Å2
MethodPISA
3
A: CalS11
C: CalS11
D: CalS11
E: CalS11
F: CalS11
H: CalS11
I: CalS11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,22539
Polymers203,6607
Non-polymers4,56432
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6320 Å2
ΔGint-62 kcal/mol
Surface area20390 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16000 Å2
ΔGint-94 kcal/mol
Surface area51790 Å2
MethodPISA
5
A: CalS11
B: CalS11
C: CalS11
E: CalS11
H: CalS11
I: CalS11
J: CalS11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,16338
Polymers203,6607
Non-polymers4,50231
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6330 Å2
ΔGint-63 kcal/mol
Surface area20940 Å2
MethodPISA
6
B: CalS11
D: CalS11
E: CalS11
F: CalS11
G: CalS11
I: CalS11
J: CalS11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,22539
Polymers203,6607
Non-polymers4,56432
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6340 Å2
ΔGint-63 kcal/mol
Surface area20520 Å2
MethodPISA
7
B: CalS11
D: CalS11
F: CalS11
G: CalS11
H: CalS11
J: CalS11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,45233
Polymers174,5666
Non-polymers3,88627
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6320 Å2
ΔGint-64 kcal/mol
Surface area20510 Å2
MethodPISA
8
B: CalS11
C: CalS11
D: CalS11
E: CalS11
F: CalS11
G: CalS11
H: CalS11
J: CalS11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,93544
Polymers232,7548
Non-polymers5,18136
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6340 Å2
ΔGint-63 kcal/mol
Surface area20360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.321, 106.080, 106.330
Angle α, β, γ (deg.)68.69, 69.63, 88.56
Int Tables number1
Space group name H-MP1
DetailsThe biological unit is a dimer.

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Components

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Protein , 1 types, 10 molecules ABCDEFGHIJ

#1: Protein
CalS11


Mass: 29094.305 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Details: Wheat Germ / Source: (gene. exp.) Micromonospora echinospora (bacteria) / Gene: calS11 / Plasmid: pET-His-Flexi / Production host: Cell-Free Synthesis (others) / References: UniProt: Q8KNF1

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Non-polymers , 5 types, 5247 molecules

#2: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical
ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C5H9NO4
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5202 / 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: 2.63 Å3/Da / Density % sol: 53.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: Protein Solution (16 mg/ml CalS11 protein, 0.0003M TCEP, 0.05M NaCl, 0.005M HEPES pH 8) mixed in a 1:1 ratio with the well solution(17.6% MEPEG5K, 160mM K-Glutamate, 100mM BisTris pH 6.5) ...Details: Protein Solution (16 mg/ml CalS11 protein, 0.0003M TCEP, 0.05M NaCl, 0.005M HEPES pH 8) mixed in a 1:1 ratio with the well solution(17.6% MEPEG5K, 160mM K-Glutamate, 100mM BisTris pH 6.5)Cryoprotected with 20% Ethylene Glycol, 17.6% MEPEG5K, 160mM KGlutamate, 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: 21-ID-D / Wavelength: 0.9794 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 26, 2011 / 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: 1.55→50 Å / Num. obs: 417415 / % possible obs: 96.8 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 10
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.55-1.583.80.297194.6
1.58-1.613.80.268195
1.61-1.643.90.246195.3
1.64-1.673.90.22195.4
1.67-1.713.90.202195.6
1.71-1.753.90.181195.8
1.75-1.793.90.165196
1.79-1.843.90.146196.2
1.84-1.893.90.136196.4
1.89-1.953.90.124196.6
1.95-2.023.90.11196.8
2.02-2.13.90.099197
2.1-2.23.90.093197.3
2.2-2.323.90.089197.5
2.32-2.463.90.081197.8
2.46-2.653.90.078198
2.65-2.923.90.072198.4
2.92-3.343.90.062198.7
3.34-4.213.90.055199
4.21-503.80.057199.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→43.101 Å / Occupancy max: 1 / Occupancy min: 0.08 / SU ML: 0.18 / σ(F): 0.17 / Phase error: 17.28 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.173 1875 0.46 %
Rwork0.1464 --
obs0.1466 412070 95.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 67.636 Å2 / ksol: 0.346 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.5644 Å2-1.338 Å20.1675 Å2
2---4.0925 Å2-2.0628 Å2
3---1.528 Å2
Refinement stepCycle: LAST / Resolution: 1.55→43.101 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20100 0 430 5202 25732
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01922366
X-RAY DIFFRACTIONf_angle_d1.71630611
X-RAY DIFFRACTIONf_dihedral_angle_d12.368537
X-RAY DIFFRACTIONf_chiral_restr0.1193294
X-RAY DIFFRACTIONf_plane_restr0.014116
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5497-1.59160.25141290.166130142X-RAY DIFFRACTION91
1.5916-1.63840.23481460.153630534X-RAY DIFFRACTION92
1.6384-1.69130.2211330.144830739X-RAY DIFFRACTION93
1.6913-1.75180.21091520.141330979X-RAY DIFFRACTION94
1.7518-1.82190.17271390.137431255X-RAY DIFFRACTION95
1.8219-1.90480.2081500.138431439X-RAY DIFFRACTION95
1.9048-2.00520.16131370.141231633X-RAY DIFFRACTION96
2.0052-2.13090.16551430.141531752X-RAY DIFFRACTION96
2.1309-2.29540.16581550.143131972X-RAY DIFFRACTION97
2.2954-2.52640.16551410.142632196X-RAY DIFFRACTION97
2.5264-2.89190.19181540.152232299X-RAY DIFFRACTION98
2.8919-3.64320.14861310.142832570X-RAY DIFFRACTION99
3.6432-43.1180.14781650.154432685X-RAY DIFFRACTION99

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