PDB-5bp7: Crystal structure of SAM-dependent methyltransferase from Geobact...

ID or keywords:

Entry

Database: PDB / ID: 5bp7

Title

Crystal structure of SAM-dependent methyltransferase from Geobacter sulfurreducens in complex with S-Adenosyl-L-homocysteine

Components

SAM-dependent methyltransferase

Keywords

TRANSFERASE /

Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC

Function / homology

Function and homology information

methyltransferase activity /

Biological species

Geobacter sulfurreducens (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.1 Å

Authors

Kutner, J. / Shabalin, I.G. / Mason, D.V. / Handing, K.B. / Gasiorowska, O.A. / Bonanno, J. / Seidel, R. / Almo, S.C. / Minor, W. / New York Structural Genomics Research Consortium (NYSGRC)

Funding support

United States, 1items

Citation

Journal: to be published
Title: Crystal structure of SAM-dependent methyltransferase from Geobacter sulfurreducens in complex with S-Adenosyl-L-homocysteine
Authors: Kutner, J. / Shabalin, I.G. / Mason, D. / Handing, K.B. / Gasiorowska, O.A. / Bonanno, J. / Seidel, R. / Almo, S.C. / Minor, W.

History

Deposition	May 27, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 10, 2015	Provider: repository / Type: Initial release
Revision 1.1	Nov 22, 2017	Group: Derived calculations / Refinement description / Source and taxonomy Category: entity_src_gen / pdbx_struct_oper_list / software Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2	Apr 13, 2022	Group: Database references / Structure summary / Category: audit_author / citation_author / database_2 Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5bp7.cif.gz	301.1 KB	Display	PDBx/mmCIF format
PDB format	pdb5bp7.ent.gz	254.6 KB	Display	PDB format
PDBx/mmJSON format	5bp7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bp/5bp7 ftp://data.pdbj.org/pub/pdb/validation_reports/bp/5bp7	HTTPS FTP

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Related structure data

Related structure data	5bp9
Similar structure data	3svz-1 2oo4-1 1l9k-d 1y8c-d 6uay-2 2giu-d 4hv3-d 4zi1-d 6atq-1 5fqt-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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
Other databases	TargetTrack: NYSGRC-030788

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: SAM-dependent methyltransferase

B: SAM-dependent methyltransferase

C: SAM-dependent methyltransferase

hetero molecules

91.7 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: SAM-dependent methyltransferase

hetero molecules

defined by author
30.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: SAM-dependent methyltransferase

hetero molecules

defined by author
30.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: SAM-dependent methyltransferase

hetero molecules

defined by author
30.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

A: SAM-dependent methyltransferase

hetero molecules

B: SAM-dependent methyltransferase

hetero molecules

C: SAM-dependent methyltransferase

hetero molecules

defined by software
91.7 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	89.346, 110.189, 76.681
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-512- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	C
1	3	B
2	3	C

NCS domain segments:

Dom-ID	Ens-ID	Auth asym-ID	Auth seq-ID
1	1	A	2 - 248
2	1	B	2 - 248
1	2	A	1 - 249
2	2	C	1 - 249
1	3	B	2 - 248
2	3	C	2 - 248

NCS ensembles :

ID
1
2
3

#1: Protein	SAM-dependent methyltransferase Mass: 30170.896 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacter sulfurreducens (bacteria) / Strain: ATCC 51573 / DSM 12127 / PCA / Gene: GSU2441 / Plasmid: pSGC-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: Q74AD5
#2: Chemical	ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₄H₂₀N₆O₅S
#3: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 418 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.28 Å³/Da / Density % sol: 41.01 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 ul of 15 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the MCSG Suite 1 condition #9 (0.1M HEPES, 25%w/v PEG ...Details: 0.2 ul of 15 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the MCSG Suite 1 condition #9 (0.1M HEPES, 25%w/v PEG 3350, 0.2M Magnesium Chloride, 6-Hydrate pH=7.5) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). Before crystallization protein was incubated with 5 mM S-adenosylmethionine chloride and 1/50 v/v of 1 mg/ml TEV solution at 289 K for 3 hours PH range: 7.5

Crystal

Density Matthews: 2.28 Å³/Da / Density % sol: 41.01 %

Crystal grow

Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 ul of 15 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the MCSG Suite 1 condition #9 (0.1M HEPES, 25%w/v PEG ...
PH range: 7.5

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-G / Wavelength: 0.97856 Å

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 16, 2015 / Details: Beryllium Lenses

Radiation

Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97856 Å / Relative weight: 1

Reflection

Resolution: 2.1→50 Å / Num. all: 45134 / Num. obs: 45102 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.1 % / B_iso Wilson estimate: 33.1 Å² / R_merge(I) obs: 0.123 / R_pim(I) all: 0.054 / R_rim(I) all: 0.13 / R_sym value: 0.123 / Χ²: 1.101 / Net I/av σ(I): 16.897 / Net I/σ(I): 5.1 / Num. measured all: 276539

Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique all	CC_1/2	R_pim(I) all	Χ²	% possible all	R_rim(I) all
2.1-2.14	6	0.995	1.6	2223	0.756	0.444	0.699	100
2.14-2.18	6.2	0.914		2205	0.786	0.402	0.711	100	0.999
2.18-2.22	6.2	0.819		2225	0.783	0.358	0.716	100	0.895
2.22-2.26	6.2	0.704		2243	0.847	0.308	0.725	100	0.769
2.26-2.31	6.2	0.666		2222	0.849	0.291	0.747	100	0.728
2.31-2.37	6.2	0.565		2219	0.904	0.247	0.751	100	0.618
2.37-2.42	6.2	0.502		2206	0.914	0.22	0.767	100	0.549
2.42-2.49	6.2	0.447		2261	0.922	0.195	0.788	100	0.488
2.49-2.56	6.2	0.376		2244	0.944	0.164	0.818	100	0.411
2.56-2.65	6.2	0.325		2218	0.955	0.141	0.848	100	0.355
2.65-2.74	6.2	0.27		2264	0.968	0.118	0.871	100	0.295
2.74-2.85	6.2	0.238		2207	0.973	0.104	0.904	100	0.26
2.85-2.98	6.2	0.18		2263	0.986	0.078	0.953	100	0.196
2.98-3.14	6.2	0.142		2241	0.99	0.062	1.055	100	0.155
3.14-3.33	6.2	0.105		2268	0.994	0.046	1.205	100	0.115
3.33-3.59	6.2	0.086		2264	0.995	0.038	1.353	100	0.094
3.59-3.95	6.1	0.071		2289	0.996	0.031	1.565	100	0.077
3.95-4.52	6	0.06		2280	0.997	0.027	1.732	99.8	0.066
4.52-5.7	6	0.06		2312	0.997	0.027	1.982	99.7	0.066
5.7-50	5.5	0.064		2448	0.997	0.029	2.923	99.6	0.07

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Processing

Software

Name	Version	Classification
PDB_EXTRACT	3.15	data extraction
REFMAC	5.8.0107	refinement
HKL-3000		phasing
MLPHARE		phasing
SHELX		phasing
HKL-3000		data scaling
HKL-3000		data reduction
BLU-MAX		data collection

Refinement

Method to determine structure:

SAD / Resolution: 2.1→50 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.943 / WR_factor R_free: 0.2016 / WR_factor R_work: 0.1677 / FOM work R set: 0.8287 / SU B: 11.476 / SU ML: 0.152 / SU R Cruickshank DPI: 0.2319 / SU R_free: 0.181 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.232 / ESU R Free: 0.181 / SU R_free Cruickshank DPI: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2229	2191	4.9 %	RANDOM
R_work	0.1855	-	-	-
obs	0.1873	42695	99.93 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso max: 104.51 Å² / B_iso mean: 40.658 Å² / B_iso min: 9.09 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.99 Å²	-0 Å²	-0 Å²
2-	-	-0.58 Å²	0 Å²
3-	-	-	2.57 Å²

Refinement step

Cycle: final / Resolution: 2.1→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5665	0	80	419	6164
B_iso mean	-	-	38.06	43.56	-
Num. residues	-	-	-	-	746

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.019	5883
X-RAY DIFFRACTION	r_bond_other_d	0.006	0.02	5562
X-RAY DIFFRACTION	r_angle_refined_deg	1.458	1.989	8009
X-RAY DIFFRACTION	r_angle_other_deg	1.196	3	12744
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.938	5	745
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.691	22.246	236
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.828	15	855
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.425	15	56
X-RAY DIFFRACTION	r_chiral_restr	0.075	0.2	900
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	6620
X-RAY DIFFRACTION	r_gen_planes_other	0.006	0.02	1330
X-RAY DIFFRACTION	r_mcbond_it	0.798	2.266	2992
X-RAY DIFFRACTION	r_mcbond_other	0.796	2.265	2991
X-RAY DIFFRACTION	r_mcangle_it	1.285	3.391	3730

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	28702	0.07
1	2	B	28702	0.07
2	1	A	29010	0.06
2	2	C	29010	0.06
3	1	B	28392	0.07
3	2	C	28392	0.07

LS refinement shell

Resolution: 2.1→2.154 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.29	174	-
R_work	0.276	3074	-
all	-	3248	-
obs	-	-	99.97 %

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	1.2537	1.0131	-0.236	4.0816	2.5316	2.4277	0.1926	-0.0721	0.0411	-0.1112	-0.0211	-0.2865	-0.2015	-0.0237	-0.1715	0.1704	-0.0228	0.0158	0.2546	0.0016	0.2205	27.922	-6.647	56.161
2	2.1183	-0.0081	-0.3393	2.3486	0.756	3.5653	0.0889	-0.0758	-0.0185	0.0703	-0.0592	-0.2104	-0.0721	0.2098	-0.0297	0.0905	-0.0395	-0.0249	0.2037	0.0177	0.1484	36.247	-9.497	52.311
3	1.6291	-0.5928	0.0993	1.4742	-0.0534	2.046	0.0662	-0.07	0.0706	0.0306	-0.0046	-0.2695	-0.1402	0.1645	-0.0617	0.0924	-0.0228	0.0337	0.1381	0.0011	0.1755	34.761	-4.21	46.015
4	2.0325	0.553	-0.5258	1.1219	0.5731	1.9223	0.2324	0.1754	0.2304	-0.1174	-0.0933	0.1172	-0.2372	-0.249	-0.1392	0.149	0.0168	0.0088	0.1689	0.0429	0.1292	16.333	-1.617	43.436
5	0.34	-0.1976	0.1645	0.954	0.7518	1.9552	-0.0351	-0.022	0.1105	0.0338	0.0196	-0.0477	-0.1394	-0.1113	0.0154	0.1154	-0.0205	-0.0144	0.1865	-0.0124	0.1469	19.183	-1.547	61.814
6	2.3558	-2.5502	0.3648	3.0649	0.0723	0.9316	0.0306	0.1448	0.0506	-0.0564	-0.0281	-0.0181	0.1189	0.1206	-0.0024	0.2262	-0.0348	0.0106	0.2453	0.0238	0.2626	31.024	32.028	77.029
7	2.3713	-2.2812	0.2793	3.5333	-0.3657	1.2409	0.0765	0.1122	-0.2567	-0.1589	-0.0624	0.3547	0.1819	-0.0514	-0.014	0.1461	-0.015	-0.0468	0.1463	-0.0543	0.1102	24.978	29.162	71.567
8	3.1499	-0.1374	-0.7482	4.532	0.8053	1.0748	0.0451	0.3154	0.068	-0.4341	-0.1559	0.1127	0.0132	0.0411	0.1107	0.2111	0.0279	-0.0663	0.2412	0.0159	0.0512	30.43	40.384	65.276
9	6.637	-3.0244	3.0666	2.9605	-1.0931	1.7347	0.0033	0.1681	0.3345	-0.1899	-0.168	-0.3829	0.0431	0.1793	0.1646	0.1206	-0.0339	0.0198	0.1939	0.0594	0.0998	42.276	47.107	79.712
10	1.0726	-0.8139	0.1722	2.352	-0.2799	0.3416	-0.0197	0.1398	-0.0227	-0.1078	-0.0578	-0.0814	0.0266	0.1221	0.0775	0.1385	0.0159	0.022	0.2306	0.0059	0.1159	42.53	29.795	83.166
11	16.0559	-18.2631	0.5786	20.9174	-0.536	4.9129	-0.3075	0.1493	0.1901	0.5784	-0.1113	-0.2378	0.021	-0.1029	0.4188	0.3944	0.0294	-0.0774	0.3261	0.0089	0.1153	32.876	19.709	46.211
12	1.3163	0.0418	-0.4632	0.9979	-0.5979	1.04	-0.0157	0.0392	-0.0589	0.0456	0.0382	0.0112	0.051	-0.1511	-0.0226	0.0816	-0.0103	-0.0097	0.223	0.0061	0.086	33.294	15.626	27.465
13	2.6963	-2.5546	-1.5021	9.1894	5.7154	9.0065	-0.3801	-0.8281	0.483	0.3933	0.5321	-0.4782	-0.2582	0.6454	-0.1519	0.1145	0.0586	-0.0846	0.4481	-0.0551	0.3112	50.446	32.255	30.023
14	1.0713	-0.3793	-1.0592	1.0725	0.874	2.2486	0.024	-0.1339	0.0851	0.2347	-0.0054	-0.1016	0.0706	-0.0106	-0.0187	0.1356	0.0121	-0.0103	0.2397	0.019	0.085	32.34	31.325	37.11
15	1.5208	-1.5528	-1.7299	8.0017	4.9109	5.1448	0.0863	-0.0847	0.2102	-0.0475	0.06	-0.2003	-0.1586	0.1548	-0.1462	0.0509	-0.0067	-0.0359	0.2395	0.0512	0.1319	41.592	31.78	28.39

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 36
2	X-RAY DIFFRACTION	2	A	37 - 81
3	X-RAY DIFFRACTION	3	A	82 - 123
4	X-RAY DIFFRACTION	4	A	124 - 182
5	X-RAY DIFFRACTION	5	A	183 - 249
6	X-RAY DIFFRACTION	6	B	2 - 40
7	X-RAY DIFFRACTION	7	B	41 - 87
8	X-RAY DIFFRACTION	8	B	88 - 132
9	X-RAY DIFFRACTION	9	B	133 - 182
10	X-RAY DIFFRACTION	10	B	183 - 249
11	X-RAY DIFFRACTION	11	C	0 - 9
12	X-RAY DIFFRACTION	12	C	10 - 145
13	X-RAY DIFFRACTION	13	C	146 - 176
14	X-RAY DIFFRACTION	14	C	177 - 226
15	X-RAY DIFFRACTION	15	C	227 - 249

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