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- PDB-4ymg: Crystal structure of SAM-bound Podospora anserina methyltransfera... -

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Basic information

Entry
Database: PDB / ID: 4ymg
TitleCrystal structure of SAM-bound Podospora anserina methyltransferase PaMTH1
ComponentsPutative SAM-dependent O-methyltranferase
KeywordsTRANSFERASE / Methylation
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
PHOSPHATE ION / S-ADENOSYLMETHIONINE / Putative SAM-dependent O-methyltranferase
Similarity search - Component
Biological speciesPodospora anserina (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.899 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
DepositionMar 6, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 27, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2015Group: Database references
Revision 1.2Jul 8, 2015Group: Database references
Revision 1.3Jun 12, 2019Group: Data collection / Structure summary
Category: audit_author / database_PDB_rev ...audit_author / database_PDB_rev / database_PDB_rev_record / pdbx_struct_ref_seq_depositor_info
Item: _audit_author.name / _pdbx_struct_ref_seq_depositor_info.db_seq_one_letter_code
Revision 1.4Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative SAM-dependent O-methyltranferase
B: Putative SAM-dependent O-methyltranferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1769
Polymers53,8752
Non-polymers1,3007
Water7,440413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7390 Å2
ΔGint-55 kcal/mol
Surface area18930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.040, 78.791, 82.718
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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Protein , 1 types, 2 molecules AB

#1: Protein Putative SAM-dependent O-methyltranferase


Mass: 26937.621 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 BL21(DE3) (bacteria) / References: UniProt: Q9HGR1

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Non-polymers , 5 types, 420 molecules

#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 413 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.2 M Lithium sulfate, 0.1M Bis-Tris, 25% PEG3350 / PH range: 5.5-6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 24, 2015
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.899→45.52 Å / Num. obs: 39322 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 6.63 % / Biso Wilson estimate: 22.16 Å2 / Rmerge(I) obs: 0.137 / Net I/σ(I): 12.75
Reflection shellResolution: 1.899→1.9461 Å / Redundancy: 6 % / Mean I/σ(I) obs: 2 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSxdsapp 1.1data reduction
Cootmodel building
PHASERphasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QVK

4qvk


Resolution: 1.899→41.359 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2016 1967 5 %Random selection
Rwork0.1592 ---
obs0.1605 39319 99.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.899→41.359 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3738 0 83 413 4234
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083910
X-RAY DIFFRACTIONf_angle_d0.9995302
X-RAY DIFFRACTIONf_dihedral_angle_d14.8391438
X-RAY DIFFRACTIONf_chiral_restr0.041564
X-RAY DIFFRACTIONf_plane_restr0.004675
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8986-1.94610.30621350.24052556X-RAY DIFFRACTION97
1.9461-1.99870.26621380.20672624X-RAY DIFFRACTION100
1.9987-2.05760.2511390.19462640X-RAY DIFFRACTION100
2.0576-2.1240.23371390.18152646X-RAY DIFFRACTION100
2.124-2.19990.22781400.16852652X-RAY DIFFRACTION100
2.1999-2.28790.22211390.15962634X-RAY DIFFRACTION100
2.2879-2.39210.22471390.15542654X-RAY DIFFRACTION100
2.3921-2.51820.21891390.15462641X-RAY DIFFRACTION100
2.5182-2.67590.23111410.15482684X-RAY DIFFRACTION100
2.6759-2.88250.18431400.16162656X-RAY DIFFRACTION100
2.8825-3.17240.21691420.1692697X-RAY DIFFRACTION100
3.1724-3.63130.20611420.14562697X-RAY DIFFRACTION100
3.6313-4.57410.14361440.12832731X-RAY DIFFRACTION100
4.5741-41.36880.18761500.15292840X-RAY DIFFRACTION100
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)
10.0637-0.1643-0.21830.14670.14360.18670.07070.0065-0.0539-0.0124-0.04640.164-0.1509-0.1493-0.01910.150.025-0.04620.14440.00770.1087-15.601212.7593-8.531
20.1026-0.0206-0.03060.0666-0.09230.143-0.00210.1217-0.25190.00020.0311-0.0465-0.023-0.05320.00050.1568-0.0297-0.00040.1622-0.03910.1618-6.742612.4542-12.1164
30.24920.20190.14470.28820.44030.722-0.21980.1026-0.016-0.39160.1534-0.0434-0.35950.2161-0.04310.2157-0.05960.0230.1736-0.02720.14151.842712.6089-21.8828
40.15080.15140.15980.17920.02720.49250.06090.0066-0.0652-0.06980.0004-0.07520.02160.11680.00380.13490.0130.01820.1583-0.05070.18475.36442.0259-12.6067
50.3197-0.0197-0.41740.01160.02070.4921-0.006-0.0767-0.15910.0370.0254-0.09790.1449-0.01340.00070.12170.0057-0.01390.1063-0.02080.1755-3.891-4.6924-6.9392
60.0513-0.04310.02130.18840.13140.13280.07280.07330.04240.1533-0.02720.1130.1628-0.0756-0.00060.179-0.0094-0.0170.14360.03660.1398-12.3073-3.5111.0449
70.04410.0586-0.00440.05260.0044-0.0052-0.0073-0.037-0.1565-0.0291-0.03510.01360.28260.0208-0.00010.20990.0298-0.0320.1830.04960.20781.0993-3.014217.4382
80.2731-0.19720.05960.20560.11570.37370.0454-0.0865-0.06730.1480.0076-0.11830.10430.105200.15020.0125-0.03060.1699-0.00790.15193.45238.818814.2742
90.61470.3103-0.2360.61390.03920.1637-0.0807-0.1413-0.14760.3845-0.0975-0.43580.21920.1092-0.04970.24490.0072-0.06850.28340.07380.1954.15056.445227.8733
100.04640.0013-0.07420.1876-0.15070.41830.0396-0.07440.05310.15750.0262-0.1349-0.12910.25050.06170.147-0.0159-0.03430.1733-0.01320.15333.495719.08818.9544
110.1907-0.00430.15880.2511-0.01760.53520.0056-0.00310.0220.07320.0371-0.0461-0.0521-0.05320.05260.1103-0.00720.00710.10460.0040.0946-9.965716.920710.1088
120.3031-0.1217-0.04870.06680.02130.20480.00620.03340.1445-0.10670.17550.1521-0.0025-0.13440.05160.11640.0065-0.00260.15190.02350.1096-18.204216.02112.0361
130.1328-0.00390.1304-0.0047-0.01180.0544-0.03450.07430.10690.02080.07910.1834-0.0415-0.0442-00.1194-0.01270.0170.0957-0.00030.1371-3.13822.2013-0.067
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 41 )
2X-RAY DIFFRACTION2chain 'A' and (resid 42 through 64 )
3X-RAY DIFFRACTION3chain 'A' and (resid 65 through 133 )
4X-RAY DIFFRACTION4chain 'A' and (resid 134 through 178 )
5X-RAY DIFFRACTION5chain 'A' and (resid 179 through 235 )
6X-RAY DIFFRACTION6chain 'B' and (resid 2 through 22 )
7X-RAY DIFFRACTION7chain 'B' and (resid 23 through 41 )
8X-RAY DIFFRACTION8chain 'B' and (resid 42 through 100 )
9X-RAY DIFFRACTION9chain 'B' and (resid 101 through 114 )
10X-RAY DIFFRACTION10chain 'B' and (resid 115 through 146 )
11X-RAY DIFFRACTION11chain 'B' and (resid 147 through 190 )
12X-RAY DIFFRACTION12chain 'B' and (resid 191 through 213 )
13X-RAY DIFFRACTION13chain 'B' and (resid 214 through 240 )

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