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- PDB-4htf: Crystal structure of S-adenosylmethionine-dependent methyltransfe... -

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Basic information

Entry
Database: PDB / ID: 4htf
TitleCrystal structure of S-adenosylmethionine-dependent methyltransferase from Escherichia coli in complex with S-adenosylmethionine.
Components(S-adenosylmethionine-dependent ...) x 2
KeywordsTRANSFERASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


tRNA (5-carboxymethoxyuridine(34)-5-O)-methyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases
Similarity search - Function
tRNA 5-carboxymethoxyuridine methyltransferase / Methyltransferase domain / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / BETA-MERCAPTOETHANOL / S-ADENOSYLMETHIONINE / tRNA 5-carboxymethoxyuridine methyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsFilippova, E.V. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Jedrzejczak, R. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of S-adenosylmethionine-dependent methyltransferase from Escherichia coli in complex with S-adenosylmethionine.
Authors: Filippova, E.V. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Jedrzejczak, R. / Joachimiak, A. / Anderson, W.F.
History
DepositionNov 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 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: S-adenosylmethionine-dependent methyltransferase
B: S-adenosylmethionine-dependent methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,4348
Polymers66,3082
Non-polymers1,1266
Water6,648369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-50 kcal/mol
Surface area22130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.537, 63.466, 136.881
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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S-adenosylmethionine-dependent ... , 2 types, 2 molecules AB

#1: Protein S-adenosylmethionine-dependent methyltransferase


Mass: 33162.066 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: Sakai, O157:H7 / Gene: BAB34427, ECs1004, smtA, Z1268 / Plasmid: pMCSG57 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) magic / References: UniProt: Q8XDG3
#2: Protein S-adenosylmethionine-dependent methyltransferase


Mass: 33146.066 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: Sakai, O157:H7 / Gene: BAB34427, ECs1004, smtA, Z1268 / Plasmid: pMCSG57 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) magic / References: UniProt: Q8XDG3

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Non-polymers , 5 types, 375 molecules

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


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 369 / 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: 1.98 Å3/Da / Density % sol: 37.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Ammonium sulfate, 0.1 M Bis-Tris, 25% PEG 3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 4, 2012 / Details: Beryllium lenses
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. all: 70394 / Num. obs: 70394 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 27.5 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 21.9
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 3.3 / Num. unique all: 3508 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
HKL-3000phasing
REFMAC5.7.0029refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.6→28.81 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.438 / SU ML: 0.061 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20144 3553 5.1 %RANDOM
Rwork0.17913 ---
obs0.18025 66760 99.71 %-
all-66760 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.492 Å2
Baniso -1Baniso -2Baniso -3
1-2.29 Å20 Å2-0 Å2
2--0.24 Å2-0 Å2
3----2.53 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.6→28.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3929 0 72 369 4370
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0194173
X-RAY DIFFRACTIONr_bond_other_d0.0010.023952
X-RAY DIFFRACTIONr_angle_refined_deg1.8611.9815663
X-RAY DIFFRACTIONr_angle_other_deg0.84139057
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.4235506
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.11923.725204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.7515647
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.8061533
X-RAY DIFFRACTIONr_chiral_restr0.1180.2610
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024767
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021014
LS refinement shellResolution: 1.599→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 281 -
Rwork0.227 4796 -
obs--98.91 %
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)
11.4422-0.1542.1050.2069-1.726818.6980.1577-0.183-0.2655-0.1236-0.04160.00120.28090.9111-0.11610.34840.03110.00850.29820.050.294727.9923-8.302331.491
21.49130.20271.25050.4601-0.0981.27140.1205-0.3666-0.23070.10990.07110.06290.1654-0.4095-0.19160.2927-0.03210.07870.29250.07310.277410.75281.852225.2183
33.8792-0.705-0.092.44641.29125.2788-0.1095-0.3112-0.92060.2790.10930.23670.7797-0.34260.00020.2636-0.140.06330.14570.11220.45215.212-8.155217.8837
41.4993-0.00470.25070.7225-0.02480.9637-0.0329-0.1022-0.20310.04220.05490.11660.1053-0.2106-0.0220.0221-0.00980.00250.10240.01390.090912.65937.6511.5785
50.811-0.15530.5380.5323-0.03521.4586-0.0643-0.0618-0.09210.08190.04410.07070.0994-0.14350.02020.0430.01870.00740.07580.00490.101120.400510.64618.8296
63.53620.8559-1.30820.2315-0.52332.287-0.136-0.283-0.4404-0.0545-0.0789-0.12060.22130.21210.21490.05930.03910.02640.13150.01350.161252.269612.67363.106
71.13280.0722-1.87980.4331.10366.62020.4705-0.0490.2319-0.29530.0984-0.042-1.71580.3946-0.56890.4717-0.10430.15830.0741-0.02670.158341.794237.83068.8563
85.23640.2946-0.72653.61510.15163.50840.5271-0.21270.2843-0.3348-0.0331-0.3731-1.00860.9483-0.4940.4095-0.31550.20760.2999-0.11150.210151.792144.013516.1393
90.4918-0.5207-0.66481.5251.7962.78710.2026-0.10170.1209-0.47040.0653-0.2588-0.73490.2554-0.26790.2071-0.06090.05930.0859-0.04230.119436.743335.148322.6869
100.6245-0.1415-0.64910.5290.80172.72660.07030.01710.0773-0.1001-0.0425-0.0435-0.3751-0.0145-0.02790.06050.0186-0.00080.0652-0.01690.107134.08926.848714.6255
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 20
2X-RAY DIFFRACTION2A21 - 59
3X-RAY DIFFRACTION3A60 - 107
4X-RAY DIFFRACTION4A108 - 173
5X-RAY DIFFRACTION5A174 - 256
6X-RAY DIFFRACTION6B1 - 20
7X-RAY DIFFRACTION7B21 - 59
8X-RAY DIFFRACTION8B60 - 107
9X-RAY DIFFRACTION9B108 - 172
10X-RAY DIFFRACTION10B181 - 255

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