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- PDB-4qvk: Apo-crystal structure of Podospora anserina methyltransferase PaMTH1 -

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Basic information

Entry
Database: PDB / ID: 4qvk
TitleApo-crystal structure of Podospora anserina methyltransferase PaMTH1
ComponentsPaMTH1 Methyltransferase
KeywordsTRANSFERASE / Methylase / S-adenosylmethionine
Function / homology
Function and homology information


S-adenosylmethionine-dependent methyltransferase activity / O-methyltransferase activity / methylation
Similarity search - Function
O-methyltransferase / Class I-like SAM-dependent O-methyltransferase / SAM-dependent O-methyltransferase class I-type profile. / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Putative SAM-dependent O-methyltranferase
Similarity search - Component
Biological speciesPodospora anserina (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.97 Å
AuthorsKudlinzki, D. / Linhard, V.L. / Chatterjee, D. / Saxena, K. / Sreeramulu, S. / Schwalbe, H.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structure and Biophysical Characterization of the S-Adenosylmethionine-dependent O-Methyltransferase PaMTH1, a Putative Enzyme Accumulating during Senescence of Podospora anserina.
Authors: Chatterjee, D. / Kudlinzki, D. / Linhard, V. / Saxena, K. / Schieborr, U. / Gande, S.L. / Wurm, J.P. / Wohnert, J. / Abele, R. / Rogov, V.V. / Dotsch, V. / Osiewacz, H.D. / Sreeramulu, S. / Schwalbe, H.
History
DepositionJul 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: Database references
Revision 1.2Jul 15, 2015Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PaMTH1 Methyltransferase
B: PaMTH1 Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3904
Polymers54,2662
Non-polymers1242
Water7,332407
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6270 Å2
ΔGint-37 kcal/mol
Surface area19370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.384, 79.719, 84.393
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PaMTH1 Methyltransferase


Mass: 27132.818 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Podospora anserina (fungus) / Gene: mth1 / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HGR1
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 407 / 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: 2.27 Å3/Da / Density % sol: 45.92 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% PEG 3350, 0.1M Bis-Tris, 0.2M NaCl, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.97626, 0.98401, 0.98004, 0.97989
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 29, 2013
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.976261
20.984011
30.980041
40.979891
ReflectionResolution: 1.97→84.39 Å / Num. obs: 35566 / Observed criterion σ(F): 1.8 / Redundancy: 5.1 % / Biso Wilson estimate: 37.7 Å2 / Rmerge(I) obs: 0.067

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementMethod to determine structure: MAD / Resolution: 1.97→26.267 Å / SU ML: 0.21 / σ(F): 1.34 / Phase error: 21.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2064 1587 4.48 %
Rwork0.1737 --
obs0.1752 35407 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.97→26.267 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3712 0 8 407 4127
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123808
X-RAY DIFFRACTIONf_angle_d1.2645158
X-RAY DIFFRACTIONf_dihedral_angle_d13.6931394
X-RAY DIFFRACTIONf_chiral_restr0.058550
X-RAY DIFFRACTIONf_plane_restr0.006666
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.03360.30441560.26793011X-RAY DIFFRACTION100
2.0336-2.10620.2891490.24793037X-RAY DIFFRACTION100
2.1062-2.19050.24971450.21593019X-RAY DIFFRACTION100
2.1905-2.29010.21881330.20193081X-RAY DIFFRACTION100
2.2901-2.41080.27161310.19753069X-RAY DIFFRACTION100
2.4108-2.56170.26241450.18993069X-RAY DIFFRACTION100
2.5617-2.75930.23671450.17983053X-RAY DIFFRACTION100
2.7593-3.03660.23751580.18263079X-RAY DIFFRACTION100
3.0366-3.47520.19531250.16543144X-RAY DIFFRACTION100
3.4752-4.37510.15041570.14163128X-RAY DIFFRACTION100
4.3751-26.26950.17571430.15293130X-RAY DIFFRACTION95
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)
15.6625-1.12080.80236.73460.63053.1479-0.1563-0.343-0.11360.21430.12180.4721-0.0343-0.4537-0.00340.17680.02330.02130.22420.0170.218392.341832.275284.3749
22.67240.69180.5432.27330.66143.2663-0.1671-0.9107-0.17880.65160.10380.0590.45190.23570.00860.41640.16960.01560.56960.10870.2646107.701426.3696103.8871
31.8129-0.1984-0.27972.03620.79623.2289-0.0004-0.33580.14320.03150.1751-0.2577-0.35430.5766-0.0960.1951-0.03960.00940.303-0.03790.1803110.385641.890194.8822
42.1638-0.6177-0.55512.18110.34432.01830.10710.26470.2197-0.49180.00620.0184-0.3674-0.0148-0.11050.3439-0.030.00550.20620.04280.2281106.948840.826575.5825
51.6522-0.2293-0.493.76160.25243.44720.1110.37920.0118-0.59960.0107-0.0702-0.05940.4194-0.08860.36650.02550.06820.33460.00490.2638116.620528.031165.2219
62.9007-0.36960.41361.7046-0.18291.98240.04830.1159-0.3482-0.1188-0.0020.04270.1408-0.0568-0.04130.2030.0036-0.00910.15820.01130.2197101.939722.427375.8135
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 22 )
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 133 )
3X-RAY DIFFRACTION3chain 'A' and (resid 134 through 236 )
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 64 )
5X-RAY DIFFRACTION5chain 'B' and (resid 65 through 133 )
6X-RAY DIFFRACTION6chain 'B' and (resid 134 through 236 )

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