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- PDB-2igt: Crystal Structure of the SAM Dependent Methyltransferase from Agr... -

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Basic information

Entry
Database: PDB / ID: 2igt
TitleCrystal Structure of the SAM Dependent Methyltransferase from Agrobacterium tumefaciens
ComponentsSAM dependent methyltransferase
KeywordsTRANSFERASE / alpha-beta sandwich / beta-barrel / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


methyltransferase activity / methylation
Similarity search - Function
S-adenosylmethionine-dependent methyltransferase / S-adenosylmethionine-dependent methyltransferase / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich ...S-adenosylmethionine-dependent methyltransferase / S-adenosylmethionine-dependent methyltransferase / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / FORMIC ACID / S-ADENOSYLMETHIONINE / SAM dependent methyltransferase / :
Similarity search - Component
Biological speciesAgrobacterium tumefaciens str. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.89 Å
AuthorsKim, Y. / Joachimiak, A. / Xu, X. / Gu, J. / Edwards, A. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of the SAM Dependent Methyltransferase from Agrobacterium tumefaciens
Authors: Kim, Y. / Joachimiak, A. / Xu, X. / Gu, J. / Edwards, A. / Savchenko, A.
History
DepositionSep 25, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SAM dependent methyltransferase
B: SAM dependent methyltransferase
C: SAM dependent methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,35621
Polymers112,2943
Non-polymers2,06218
Water16,934940
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: SAM dependent methyltransferase
B: SAM dependent methyltransferase
C: SAM dependent methyltransferase
hetero molecules

A: SAM dependent methyltransferase
B: SAM dependent methyltransferase
C: SAM dependent methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,71142
Polymers224,5876
Non-polymers4,12436
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
Buried area23150 Å2
ΔGint-66 kcal/mol
Surface area67090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.941, 145.555, 204.895
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein SAM dependent methyltransferase


Mass: 37431.188 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens str. (bacteria)
Species: Agrobacterium tumefaciens / Strain: C58 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: Q8UIF7, UniProt: A9CKD6*PLUS

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Non-polymers , 5 types, 958 molecules

#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H4O2
#5: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: CH2O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 940 / 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: 2.79 Å3/Da / Density % sol: 55.84 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1M sodium acetate 4.6, 3.2M sodium formate, 4% glycerol, 5mM SAM, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97937
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 4, 2006 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97937 Å / Relative weight: 1
ReflectionResolution: 1.89→42.83 Å / Num. all: 99837 / Num. obs: 99837 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 117.6 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 11.5
Reflection shellResolution: 1.89→1.96 Å / Redundancy: 14.3 % / Rmerge(I) obs: 0.692 / Mean I/σ(I) obs: 4.3 / Num. unique all: 9691 / % possible all: 98.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
SHELXCDphasing
SHELXDphasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
MLPHAREphasing
Cootmodel building
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.89→42.83 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 4.914 / SU ML: 0.078 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.133 / ESU R Free: 0.121
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.19236 10017 10 %RANDOM
Rwork0.16231 ---
all0.16534 89666 --
obs0.16534 89666 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.174 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20 Å20 Å2
2---1.33 Å20 Å2
3---0.66 Å2
Refinement stepCycle: LAST / Resolution: 1.89→42.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7395 0 138 940 8473
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0218555
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3961.96211660
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6551078
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.0122.787409
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.066151398
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0751584
X-RAY DIFFRACTIONr_chiral_restr0.0990.21209
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026776
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2170.24235
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.25638
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2907
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.2175
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.230.272
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8741.55381
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.29128332
X-RAY DIFFRACTIONr_scbond_it2.04433742
X-RAY DIFFRACTIONr_scangle_it3.0934.53328
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.892→1.941 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 669 -
Rwork0.221 6343 -
obs-6343 96.13 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.3668-0.3108-1.31851.93970.56411.3093-0.1454-0.1298-0.08610.12030.2156-0.14860.4510.3501-0.07020.01160.0177-0.0082-0.008-0.02430.074684.852438.143234.5704
20.3665-0.0669-0.33981.3591-0.41970.6514-0.00010.0420.0179-0.15250.04090.08930.0325-0.0672-0.04080.0505-0.0638-0.02880.04070.0007-0.027172.254854.826115.8923
30.8390.16-0.12280.8063-0.16091.3593-0.0608-0.04780.01340.04020.07690.06380.0887-0.1624-0.01610.0155-0.03360.01950.01060.01870.037867.082945.036736.2435
40.51540.0479-0.57321.3234-0.58181.343-0.06510.0198-0.1369-0.08860.0535-0.04420.18990.05640.01150.0371-0.0230.0147-0.0028-0.0160.04182.372741.399226.6996
50.9547-0.17630.44932.57140.4631.52780.0190.20650.0977-0.3773-0.0747-0.0779-0.1476-0.22850.05570.0115-0.0068-0.00590.06840.0703-0.005869.804293.054614.7972
61.57980.4644-0.98331.6952-0.93892.10580.0513-0.05510.12610.10.01720.0957-0.06470.0245-0.0684-0.04260.04060.023-0.0438-0.01070.023367.039698.58248.1149
70.4723-0.057-0.28630.80450.44251.1642-0.03020.17610.0269-0.1012-0.01840.1557-0.0317-0.26870.0485-0.02830.0066-0.03450.07140.02050.040160.096589.106224.8551
81.3456-1.50780.98612.312-1.5012.7483-0.2014-0.06990.07320.35320.085-0.0143-0.21450.01250.11640.050.01810.0061-0.043-0.02560.016773.310783.919573.7327
91.20410.53080.75121.73750.69322.58460.05960.0833-0.25080.03390.0235-0.05990.14560.0357-0.08310.04030.0210.0182-0.05790.00950.060278.640849.767862.3897
100.6432-0.24180.20071.6225-0.18080.5696-0.0493-0.0273-0.08250.120.05240.27130.0093-0.1061-0.0031-0.00020.01950.0683-0.02250.0170.070161.075970.794165.8435
110.4922-0.84870.37942.30010.02610.8458-0.0553-0.09080.040.27940.0018-0.0125-0.0205-0.0460.05350.07030.02740.0253-0.03240.00940.007376.238572.957874.3299
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-6 - 2115 - 42
2X-RAY DIFFRACTION2AA22 - 13443 - 155
3X-RAY DIFFRACTION3AA135 - 240156 - 261
4X-RAY DIFFRACTION4AA241 - 309262 - 330
5X-RAY DIFFRACTION5BB-6 - 2115 - 42
6X-RAY DIFFRACTION6BB22 - 8843 - 109
7X-RAY DIFFRACTION7BB89 - 309110 - 330
8X-RAY DIFFRACTION8CC-6 - 2115 - 42
9X-RAY DIFFRACTION9CC22 - 8743 - 108
10X-RAY DIFFRACTION10CC88 - 253109 - 274
11X-RAY DIFFRACTION11CC254 - 309275 - 330

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