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

ID or keywords:

Entry

Database: PDB / ID: 4ymg

Title

Crystal structure of SAM-bound Podospora anserina methyltransferase PaMTH1

Components

Putative SAM-dependent O-methyltranferase

Keywords

TRANSFERASE / Methylation

Function / homology

Function and homology information

S-adenosylmethionine-dependent methyltransferase activity / O-methyltransferase activity / methylation
Similarity search - Function

Biological species

Podospora anserina (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.899 Å

Authors

Kudlinzki, D. / Linhard, V.L. / Chatterjee, D. / Saxena, K. / Sreeramulu, S. / Schwalbe, H.

Citation

Journal: 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

Deposition	Mar 6, 2015	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	May 27, 2015	Provider: repository / Type: Initial release
Revision 1.1	Jun 3, 2015	Group: Database references
Revision 1.2	Jul 8, 2015	Group: Database references
Revision 1.3	Jun 12, 2019	Group: 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 1.4	Jan 10, 2024	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4ymg.cif.gz	209 KB	Display	PDBx/mmCIF format
PDB format	pdb4ymg.ent.gz	165.1 KB	Display	PDB format
PDBx/mmJSON format	4ymg.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4ymg_validation.pdf.gz	915.7 KB	Display	wwPDB validaton report
Full document	4ymg_full_validation.pdf.gz	916.9 KB	Display
Data in XML	4ymg_validation.xml.gz	23.4 KB	Display
Data in CIF	4ymg_validation.cif.gz	34.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ym/4ymg ftp://data.pdbj.org/pub/pdb/validation_reports/ym/4ymg	HTTPS FTP

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Related structure data

Related structure data	4qvkSC 4ymhC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4ny1-d 6bzz-2 2oa8-d 3r9j-3 2o4i-d 4ymh-2 1ryz-4 6l90-d 2xj9-d 3bt7-2 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#139 - Jul 2011 DNA Methyltransferase similarity (1)

Deposited unit

A: Putative SAM-dependent O-methyltranferase

B: Putative SAM-dependent O-methyltranferase

hetero molecules

55.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

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 number	19
Space group name H-M	P2₁2₁2₁

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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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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.33 Å³/Da / Density % sol: 47 %
Crystal grow	Temperature: 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

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

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Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: 1.9_1692)	refinement
XDS	xdsapp 1.1	data reduction
Coot		model building
PHASER		phasing
Aimless		data scaling

Refinement

Method 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

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2016	1967	5 %	Random selection
R_work	0.1592	-	-	-
obs	0.1605	39319	99.75 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.899→41.359 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3738	0	83	413	4234

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	3910
X-RAY DIFFRACTION	f_angle_d	0.999	5302
X-RAY DIFFRACTION	f_dihedral_angle_d	14.839	1438
X-RAY DIFFRACTION	f_chiral_restr	0.041	564
X-RAY DIFFRACTION	f_plane_restr	0.004	675

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.8986-1.9461	0.3062	135	0.2405	2556	X-RAY DIFFRACTION	97
1.9461-1.9987	0.2662	138	0.2067	2624	X-RAY DIFFRACTION	100
1.9987-2.0576	0.251	139	0.1946	2640	X-RAY DIFFRACTION	100
2.0576-2.124	0.2337	139	0.1815	2646	X-RAY DIFFRACTION	100
2.124-2.1999	0.2278	140	0.1685	2652	X-RAY DIFFRACTION	100
2.1999-2.2879	0.2221	139	0.1596	2634	X-RAY DIFFRACTION	100
2.2879-2.3921	0.2247	139	0.1554	2654	X-RAY DIFFRACTION	100
2.3921-2.5182	0.2189	139	0.1546	2641	X-RAY DIFFRACTION	100
2.5182-2.6759	0.2311	141	0.1548	2684	X-RAY DIFFRACTION	100
2.6759-2.8825	0.1843	140	0.1616	2656	X-RAY DIFFRACTION	100
2.8825-3.1724	0.2169	142	0.169	2697	X-RAY DIFFRACTION	100
3.1724-3.6313	0.2061	142	0.1456	2697	X-RAY DIFFRACTION	100
3.6313-4.5741	0.1436	144	0.1283	2731	X-RAY DIFFRACTION	100
4.5741-41.3688	0.1876	150	0.1529	2840	X-RAY DIFFRACTION	100

Refinement TLS params.

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

ID	L11 (°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)
1	0.0637	-0.1643	-0.2183	0.1467	0.1436	0.1867	0.0707	0.0065	-0.0539	-0.0124	-0.0464	0.164	-0.1509	-0.1493	-0.0191	0.15	0.025	-0.0462	0.1444	0.0077	0.1087	-15.6012	12.7593	-8.531
2	0.1026	-0.0206	-0.0306	0.0666	-0.0923	0.143	-0.0021	0.1217	-0.2519	0.0002	0.0311	-0.0465	-0.023	-0.0532	0.0005	0.1568	-0.0297	-0.0004	0.1622	-0.0391	0.1618	-6.7426	12.4542	-12.1164
3	0.2492	0.2019	0.1447	0.2882	0.4403	0.722	-0.2198	0.1026	-0.016	-0.3916	0.1534	-0.0434	-0.3595	0.2161	-0.0431	0.2157	-0.0596	0.023	0.1736	-0.0272	0.1415	1.8427	12.6089	-21.8828
4	0.1508	0.1514	0.1598	0.1792	0.0272	0.4925	0.0609	0.0066	-0.0652	-0.0698	0.0004	-0.0752	0.0216	0.1168	0.0038	0.1349	0.013	0.0182	0.1583	-0.0507	0.1847	5.3644	2.0259	-12.6067
5	0.3197	-0.0197	-0.4174	0.0116	0.0207	0.4921	-0.006	-0.0767	-0.1591	0.037	0.0254	-0.0979	0.1449	-0.0134	0.0007	0.1217	0.0057	-0.0139	0.1063	-0.0208	0.1755	-3.891	-4.6924	-6.9392
6	0.0513	-0.0431	0.0213	0.1884	0.1314	0.1328	0.0728	0.0733	0.0424	0.1533	-0.0272	0.113	0.1628	-0.0756	-0.0006	0.179	-0.0094	-0.017	0.1436	0.0366	0.1398	-12.3073	-3.511	1.0449
7	0.0441	0.0586	-0.0044	0.0526	0.0044	-0.0052	-0.0073	-0.037	-0.1565	-0.0291	-0.0351	0.0136	0.2826	0.0208	-0.0001	0.2099	0.0298	-0.032	0.183	0.0496	0.2078	1.0993	-3.0142	17.4382
8	0.2731	-0.1972	0.0596	0.2056	0.1157	0.3737	0.0454	-0.0865	-0.0673	0.148	0.0076	-0.1183	0.1043	0.1052	0	0.1502	0.0125	-0.0306	0.1699	-0.0079	0.1519	3.4523	8.8188	14.2742
9	0.6147	0.3103	-0.236	0.6139	0.0392	0.1637	-0.0807	-0.1413	-0.1476	0.3845	-0.0975	-0.4358	0.2192	0.1092	-0.0497	0.2449	0.0072	-0.0685	0.2834	0.0738	0.195	4.1505	6.4452	27.8733
10	0.0464	0.0013	-0.0742	0.1876	-0.1507	0.4183	0.0396	-0.0744	0.0531	0.1575	0.0262	-0.1349	-0.1291	0.2505	0.0617	0.147	-0.0159	-0.0343	0.1733	-0.0132	0.1533	3.4957	19.088	18.9544
11	0.1907	-0.0043	0.1588	0.2511	-0.0176	0.5352	0.0056	-0.0031	0.022	0.0732	0.0371	-0.0461	-0.0521	-0.0532	0.0526	0.1103	-0.0072	0.0071	0.1046	0.004	0.0946	-9.9657	16.9207	10.1088
12	0.3031	-0.1217	-0.0487	0.0668	0.0213	0.2048	0.0062	0.0334	0.1445	-0.1067	0.1755	0.1521	-0.0025	-0.1344	0.0516	0.1164	0.0065	-0.0026	0.1519	0.0235	0.1096	-18.2042	16.021	12.0361
13	0.1328	-0.0039	0.1304	-0.0047	-0.0118	0.0544	-0.0345	0.0743	0.1069	0.0208	0.0791	0.1834	-0.0415	-0.0442	-0	0.1194	-0.0127	0.017	0.0957	-0.0003	0.1371	-3.138	22.2013	-0.067

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 41 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 42 through 64 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 65 through 133 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 134 through 178 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 179 through 235 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 2 through 22 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 23 through 41 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 42 through 100 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 101 through 114 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 115 through 146 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 147 through 190 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 191 through 213 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 214 through 240 )

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