PDB-4ymh: Crystal structure of SAH-bound Podospora anserina methyltransfera...

ID or keywords:

Entry

Database: PDB / ID: 4ymh

Title

Crystal structure of SAH-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: 1.876 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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Download

PDBx/mmCIF format	4ymh.cif.gz	406.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4ymh.ent.gz	334.6 KB	Display	PDB format
PDBx/mmJSON format	4ymh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4ymh_validation.pdf.gz	1.3 MB	Display	wwPDB validaton report
Full document	4ymh_full_validation.pdf.gz	1.4 MB	Display
Data in XML	4ymh_validation.xml.gz	45 KB	Display
Data in CIF	4ymh_validation.cif.gz	66 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ym/4ymh ftp://data.pdbj.org/pub/pdb/validation_reports/ym/4ymh	HTTPS FTP

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Related structure data

Related structure data	4qvkSC 4ymgC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4qvk-d 2gew-d 4u2l-d 5sup-3 4ymg-d 5n5d-d 3tr6-1 6mjx-d 3gyj-d 5u6n-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Deposited unit

A: Putative SAM-dependent O-methyltranferase

B: Putative SAM-dependent O-methyltranferase

C: Putative SAM-dependent O-methyltranferase

D: Putative SAM-dependent O-methyltranferase

hetero molecules

110 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Putative SAM-dependent O-methyltranferase

B: Putative SAM-dependent O-methyltranferase

hetero molecules

defined by author&software
55 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Putative SAM-dependent O-methyltranferase

D: Putative SAM-dependent O-methyltranferase

hetero molecules

defined by author&software
54.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	84.233, 239.295, 50.558
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	B-1138- HOH
2	1	B-1160- HOH

#1: Protein	Putative SAM-dependent O-methyltranferase Mass: 26937.621 Da / Num. of mol.: 4 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
#2: Chemical	ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₄H₂₀N₆O₅S
#3: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 895 / 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: 2.4 Å³/Da / Density % sol: 48.8 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M Lithium sulfate, 0.1 M 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: 1.876→48.774 Å / Num. obs: 84455 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 6.61 % / B_iso Wilson estimate: 22.98 Å² / R_merge(I) obs: 0.117 / Net I/σ(I): 13
Reflection shell	Resolution: 1.876→1.9191 Å / Redundancy: 6 % / Mean I/σ(I) obs: 2.3 / % possible all: 97

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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: 1.876→48.774 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0.36 / Phase error: 20.13 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2044	2101	2.49 %	Random selection
R_work	0.1643	-	-	-
obs	0.1653	84451	99.49 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.876→48.774 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7450	0	132	895	8477

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	7806
X-RAY DIFFRACTION	f_angle_d	1.062	10584
X-RAY DIFFRACTION	f_dihedral_angle_d	14.424	2878
X-RAY DIFFRACTION	f_chiral_restr	0.043	1128
X-RAY DIFFRACTION	f_plane_restr	0.005	1355

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 (%)
1.8755-1.9191	0.2621	128	0.2485	5026	X-RAY DIFFRACTION	93
1.9191-1.9671	0.2733	140	0.2295	5468	X-RAY DIFFRACTION	100
1.9671-2.0203	0.2582	139	0.2128	5455	X-RAY DIFFRACTION	100
2.0203-2.0798	0.2675	138	0.1972	5411	X-RAY DIFFRACTION	100
2.0798-2.1469	0.2324	139	0.1889	5460	X-RAY DIFFRACTION	100
2.1469-2.2236	0.1976	140	0.1704	5477	X-RAY DIFFRACTION	100
2.2236-2.3127	0.2117	139	0.1685	5470	X-RAY DIFFRACTION	100
2.3127-2.4179	0.2234	140	0.1673	5488	X-RAY DIFFRACTION	100
2.4179-2.5454	0.2315	140	0.167	5481	X-RAY DIFFRACTION	100
2.5454-2.7048	0.2209	140	0.1714	5484	X-RAY DIFFRACTION	100
2.7048-2.9137	0.2113	141	0.1685	5510	X-RAY DIFFRACTION	100
2.9137-3.2068	0.2324	141	0.1687	5545	X-RAY DIFFRACTION	100
3.2068-3.6707	0.1783	142	0.1476	5579	X-RAY DIFFRACTION	100
3.6707-4.6242	0.1524	144	0.1278	5641	X-RAY DIFFRACTION	100
4.6242-48.7907	0.1878	150	0.1575	5855	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	7.3092	-1.9767	-1.0661	4.2672	0.36	4.9962	0.1394	0.533	0.3264	-0.4223	-0.1949	-0.2793	-0.0863	0.4964	-0.0333	0.1711	-0.0412	0.0045	0.226	0.0254	0.0993	33.8524	256.058	143.1935
2	1.6038	0.5717	1.0459	3.6171	0.88	2.6382	-0.2009	0.1218	0.4867	-0.1927	0.1234	-0.1623	-0.3819	0.1339	0.0515	0.2163	0.0172	-0.0432	0.1673	0.0098	0.3119	29.4296	274.4065	158.4986
3	1.8129	0.1697	-0.3366	2.3299	-0.2007	2.0373	-0.0569	-0.47	0.6698	0.4456	-0.0684	0.0367	-0.4659	-0.0286	0.1088	0.3254	0.0087	-0.0725	0.2225	-0.1142	0.3451	31.69	272.928	171.7716
4	2.7371	0.006	-1.0105	1.4475	0.1872	2.6732	-0.0755	-0.1175	0.1152	0.1764	0.0146	-0.1582	-0.0042	-0.0066	0.0633	0.1476	0.0095	-0.0367	0.1284	0.0066	0.1293	38.1259	257.7698	165.6244
5	5.883	0.0531	0.1487	4.1687	-1.2009	7.943	0.0753	0.4573	-0.0841	-0.1744	-0.0983	-0.1669	-0.0297	0.1562	0.1069	0.094	0.0135	0.007	0.1668	-0.0006	0.131	40.3266	250.0218	152.5005
6	5.4325	5.2364	2.7401	7.1999	3.0629	4.5409	0.2707	-0.0783	-0.4225	0.4357	-0.1377	-0.0761	0.3428	-0.0994	-0.164	0.152	0.0425	-0.0194	0.1851	0.0459	0.2326	28.2483	234.4744	159.8131
7	3.4715	-0.573	0.0793	6.7105	3.5126	3.0964	-0.0106	0.148	-0.3973	-0.057	-0.0319	-0.085	-0.1193	0.007	0.0221	0.13	-0.0127	-0.0032	0.2032	0.0315	0.1308	24.6869	243.5938	157.4274
8	2.824	0.0459	0.6196	3.1108	0.5038	1.277	0.0239	-0.1794	-0.2787	0.2319	-0.0437	0.1798	0.1119	-0.1008	0.0208	0.1126	-0.0146	0.0324	0.1779	0.0082	0.1381	12.3363	239.9738	157.633
9	3.9132	-0.0936	-1.2985	1.4724	0.2029	2.5237	-0.0659	0.3944	-0.1045	-0.255	0.0035	0.0759	0.117	0.0811	0.0525	0.1759	0.0082	-0.0299	0.2041	-0.0055	0.1088	20.0694	250.3566	142.6864
10	6.1572	-0.9409	0.4738	2.5063	-0.7886	2.3297	-0.129	-0.0059	0.5257	0.159	0.0308	0.0428	-0.2207	-0.1295	0.0686	0.1469	0.0101	-0.0296	0.1413	-0.0122	0.1142	17.4712	259.5277	151.1627
11	4.9797	-1.4635	-0.8046	6.832	-1.2776	6.6496	0.003	-0.0869	0.0032	0.1086	0.0057	0.8168	-0.2157	-0.4399	0.0226	0.2126	0.0264	-0.0234	0.2008	0.0132	0.4047	-24.4438	289.2635	144.5434
12	2.3726	0.1275	0.1802	6.3164	0.4185	3.1102	-0.1734	0.4766	-0.2644	-0.8263	0.0978	1.745	-0.082	-0.6462	0.0326	0.3886	0.0702	-0.2574	0.4331	0.0124	0.7368	-29.5189	274.7739	130.3551
13	2.6976	0.2953	-0.42	3.5122	-0.623	2.3611	-0.0635	0.2936	-0.1944	-0.5889	-0.019	0.5655	0.1485	-0.2042	0.082	0.2877	0.0047	-0.0811	0.2008	-0.0277	0.2667	-17.107	265.0563	133.7115
14	5.915	-2.4744	-4.6918	3.2517	2.4242	5.4229	0.0512	-0.0174	-0.0924	0.038	-0.0834	0.3409	-0.0797	-0.0293	0.0303	0.1652	0.005	-0.0375	0.1662	0.0386	0.1812	-15.4769	273.1117	147.8991
15	2.5788	0.7075	-2.819	2.8012	-0.3892	3.1029	-0.1633	-0.6434	-0.0774	0.35	0.1502	0.323	0.2555	0.1	0.0092	0.2278	0.0241	0.0236	0.1825	0.0324	0.198	-17.7354	269.5715	155.0487
16	5.9006	-2.4809	0.1472	4.7068	0.8311	3.3335	-0.1375	0.1752	0.4277	0.0903	0.0357	-0.437	0.1437	0.3057	0.0783	0.1333	0.0097	-0.0065	0.1671	0.0541	0.179	-4.7182	274.3789	144.0188
17	7.8712	-2.4521	-0.9716	5.7411	-0.7469	4.9079	0.1839	-0.585	0.3124	0.2124	0.1135	0.289	-0.3341	-0.098	-0.2257	0.1857	-0.0027	0.0328	0.1308	-0.024	0.2187	-16.951	284.0089	153.5898
18	2.0933	0.5758	-0.4037	4.3746	-1.0323	1.8738	0.2471	-0.2197	0.3969	0.0352	-0.1007	-0.7003	-0.3408	0.2435	-0.1	0.2371	-0.0417	0.0662	0.229	-0.0382	0.4722	3.1711	294.4088	141.2236
19	2.6068	-0.0237	-1.0774	3.591	-0.3023	3.0684	0.2246	0.1466	0.3424	-0.6028	-0.0396	0.0956	-0.2098	-0.0627	-0.1673	0.3365	0.0303	-0.0245	0.1561	0.0533	0.2722	-13.5745	295.4284	133.9005

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 22 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 23 through 114 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 115 through 146 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 147 through 240 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 2 through 22 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 23 through 41 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 42 through 64 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 65 through 146 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 147 through 213 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 214 through 236 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 2 through 22 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 23 through 41 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 42 through 159 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 160 through 190 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 191 through 213 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 214 through 236 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 2 through 22 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 23 through 133 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 134 through 235 )

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