PDB-6rk7: Inter-dimeric interface controls function and stability of S-meth...

ID or keywords:

Entry

Database: PDB / ID: 6rk7

Title

Inter-dimeric interface controls function and stability of S-methionine adenosyltransferase from U. urealiticum

Components

Methionine adenosyltransferase

Keywords

TRANSFERASE / synthetase

Function / homology

GMP Synthetase; Chain A, domain 3 - #10 / GMP Synthetase; Chain A, domain 3 / 2-Layer Sandwich / Alpha Beta / S-ADENOSYLMETHIONINE / :

Function and homology information

Biological species

Ureaplasma urealyticum serovar 7 str. ATCC 27819 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Shahar, A. / Zarivach, R. / Bershtein, S. / Kleiner, D. / Shmulevich, F.

Funding support

Israel, 1items

Citation

Journal: J.Mol.Biol. / Year: 2019
Title: The interdimeric interface controls function and stability of Ureaplasma urealiticum methionine S-adenosyltransferase.
Authors: Kleiner, D. / Shmulevich, F. / Zarivach, R. / Shahar, A. / Sharon, M. / Ben-Nissan, G. / Bershtein, S.

History

Deposition	Apr 30, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 25, 2019	Provider: repository / Type: Initial release
Revision 1.1	Dec 25, 2019	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2	Jan 24, 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 / refine / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6rk7.cif.gz	909.4 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	6rk7_validation.pdf.gz	3.8 MB	Display	wwPDB validaton report
Full document	6rk7_full_validation.pdf.gz	3.8 MB	Display
Data in XML	6rk7_validation.xml.gz	97.8 KB	Display
Data in CIF	6rk7_validation.cif.gz	137.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rk/6rk7 ftp://data.pdbj.org/pub/pdb/validation_reports/rk/6rk7	HTTPS FTP

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Related structure data

Related structure data	6rjsSC 6rk5C 6rkaC 6rkcC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5zre-d 2d0v-d 3ct4-4 5ydi-d 5elo-d 1fwx-d 2eq8-d 2fyi-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&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: Methionine adenosyltransferase

B: Methionine adenosyltransferase

E: Methionine adenosyltransferase

F: Methionine adenosyltransferase

G: Methionine adenosyltransferase

H: Methionine adenosyltransferase

hetero molecules

262 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	113.999, 106.139, 234.377
Angle α, β, γ (deg.)	90.00, 96.86, 90.00
Int Tables number	5
Space group name H-M	I121

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	LYS	LYS	SER	SER	A	A	4 - 375	4 - 375
2	1	LYS	LYS	SER	SER	B	B	4 - 375	4 - 375
1	2	LYS	LYS	SER	SER	A	A	4 - 375	4 - 375
2	2	LYS	LYS	SER	SER	E	C	4 - 375	4 - 375
1	3	LYS	LYS	SER	SER	A	A	4 - 375	4 - 375
2	3	LYS	LYS	SER	SER	F	D	4 - 375	4 - 375
1	4	LYS	LYS	LYS	LYS	A	A	4 - 376	4 - 376
2	4	LYS	LYS	LYS	LYS	G	E	4 - 376	4 - 376
1	5	LYS	LYS	SER	SER	A	A	4 - 375	4 - 375
2	5	LYS	LYS	SER	SER	H	F	4 - 375	4 - 375
1	6	TYR	TYR	SER	SER	B	B	3 - 375	3 - 375
2	6	TYR	TYR	SER	SER	E	C	3 - 375	3 - 375
1	7	TYR	TYR	LYS	LYS	B	B	3 - 376	3 - 376
2	7	TYR	TYR	LYS	LYS	F	D	3 - 376	3 - 376
1	8	TYR	TYR	SER	SER	B	B	3 - 375	3 - 375
2	8	TYR	TYR	SER	SER	G	E	3 - 375	3 - 375
1	9	LYS	LYS	SER	SER	B	B	4 - 375	4 - 375
2	9	LYS	LYS	SER	SER	H	F	4 - 375	4 - 375
1	10	TYR	TYR	SER	SER	E	C	3 - 375	3 - 375
2	10	TYR	TYR	SER	SER	F	D	3 - 375	3 - 375
1	11	TYR	TYR	SER	SER	E	C	3 - 375	3 - 375
2	11	TYR	TYR	SER	SER	G	E	3 - 375	3 - 375
1	12	LYS	LYS	SER	SER	E	C	4 - 375	4 - 375
2	12	LYS	LYS	SER	SER	H	F	4 - 375	4 - 375
1	13	TYR	TYR	SER	SER	F	D	3 - 375	3 - 375
2	13	TYR	TYR	SER	SER	G	E	3 - 375	3 - 375
1	14	LYS	LYS	SER	SER	F	D	4 - 375	4 - 375
2	14	LYS	LYS	SER	SER	H	F	4 - 375	4 - 375
1	15	LYS	LYS	SER	SER	G	E	4 - 375	4 - 375
2	15	LYS	LYS	SER	SER	H	F	4 - 375	4 - 375

NCS ensembles :

ID	Details
1	A, B
2	A, E
3	A, F
4	A, G
5	A, H
6	B, E
7	B, F
8	B, G
9	B, H
10	E, F
11	E, G
12	E, H
13	F, G
14	F, H
15	G, H

#1: Protein	Methionine adenosyltransferase Mass: 42880.602 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ureaplasma urealyticum serovar 7 str. ATCC 27819 (bacteria) Gene: metK, UUR7_0462 / Production host: Escherichia phage EcSzw-2 (virus) / References: UniProt: B2NE58, methionine adenosyltransferase
#2: Chemical	ChemComp-SAM / S-ADENOSYLMETHIONINE Mass: 398.437 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₁₅H₂₂N₆O₅S
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1417 / 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: 2.79 Å³/Da / Density % sol: 55.86 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M Hepes pH 7.0 and 30% Jeffamine ED-2001

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 27, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.976 Å / Relative weight: 1
Reflection	Resolution: 1.8→48.66 Å / Num. obs: 255563 / % possible obs: 99.8 % / Redundancy: 4.7 % / CC_1/2: 0.996 / R_merge(I) obs: 0.033 / Net I/σ(I): 9.4
Reflection shell	Resolution: 1.8→1.83 Å / R_merge(I) obs: 0.566 / Num. unique obs: 12581 / CC_1/2: 0.503

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0158	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6RJS

6rjs

Resolution: 1.8→48.66 Å / Cor.coef. F_o:F_c: 0.972 / Cor.coef. F_o:F_c free: 0.963 / SU B: 6.344 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.101 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.19448	12863	5 %	RANDOM
R_work	0.16886	-	-	-
obs	0.17017	242580	99.78 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 37.234 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.72 Å²	0 Å²	1.08 Å²
2-	-	-1.05 Å²	0 Å²
3-	-	-	1.46 Å²

Refinement step

Cycle: 1 / Resolution: 1.8→48.66 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	17633	0	330	1420	19383

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.023	0.019	18530
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	17207
X-RAY DIFFRACTION	r_angle_refined_deg	2.154	1.971	25146
X-RAY DIFFRACTION	r_angle_other_deg	1.122	3	40169
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.266	5	2315
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.567	25.59	830
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.031	15	3314
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.448	15	63
X-RAY DIFFRACTION	r_chiral_restr	0.154	0.2	2875
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.02	20451
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	3556
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	2.218	2.422	9104
X-RAY DIFFRACTION	r_mcbond_other	2.217	2.422	9104
X-RAY DIFFRACTION	r_mcangle_it	3.087	3.613	11372
X-RAY DIFFRACTION	r_mcangle_other	3.087	3.613	11373
X-RAY DIFFRACTION	r_scbond_it	3.149	2.794	9426
X-RAY DIFFRACTION	r_scbond_other	3.148	2.794	9427
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	4.783	4.042	13742
X-RAY DIFFRACTION	r_long_range_B_refined	6.66	30.118	21532
X-RAY DIFFRACTION	r_long_range_B_other	6.629	29.575	21210
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

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	25096	0.07
1	2	B	25096	0.07
2	1	A	24926	0.09
2	2	E	24926	0.09
3	1	A	25020	0.08
3	2	F	25020	0.08
4	1	A	25074	0.08
4	2	G	25074	0.08
5	1	A	25046	0.08
5	2	H	25046	0.08
6	1	B	25064	0.08
6	2	E	25064	0.08
7	1	B	25084	0.07
7	2	F	25084	0.07
8	1	B	24940	0.08
8	2	G	24940	0.08
9	1	B	25056	0.08
9	2	H	25056	0.08
10	1	E	25116	0.08
10	2	F	25116	0.08
11	1	E	25212	0.08
11	2	G	25212	0.08
12	1	E	25118	0.08
12	2	H	25118	0.08
13	1	F	25050	0.07
13	2	G	25050	0.07
14	1	F	24902	0.07
14	2	H	24902	0.07
15	1	G	24860	0.07
15	2	H	24860	0.07

LS refinement shell

Resolution: 1.8→1.847 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.379	947	-
R_work	0.368	17744	-
obs	-	-	99.15 %

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	0.194	0.0068	-0.1972	0.0367	0.0631	0.3553	0.0162	0.0155	0.0183	0.016	0.0287	-0.0146	0.0309	-0.007	-0.0449	0.1069	-0.0278	0.0278	0.1216	-0.0084	0.1128	-44.9093	0.2509	-24.4186
2	0.1904	0.1366	-0.185	0.2362	0.0351	0.4082	0.1252	0.0525	0.1067	0.003	0.0589	0.0309	-0.212	-0.0604	-0.1841	0.146	0.0068	0.087	0.0755	0.0453	0.1372	-52.1806	22.675	-26.7796
3	0.1282	-0.0433	-0.1163	0.2621	0.0103	0.2416	0.0487	0.0479	-0.0196	-0.0152	-0.0347	0.0164	-0.0692	-0.0143	-0.014	0.1081	0.0029	0.0175	0.1117	-0.0127	0.1138	-20.146	-31.9845	-48.099
4	0.2117	0.0647	-0.056	0.2225	0.0114	0.1866	0.0014	-0.1038	-0.0748	0.0304	-0.0183	0.0431	-0.0363	0.0101	0.0169	0.1008	-0.0149	0.0276	0.1313	0.0068	0.1046	-21.9098	-42.2505	-26.8793
5	0.2761	0.1995	-0.1511	0.3676	-0.0423	0.1079	0.0914	-0.2406	-0.0962	0.0306	-0.1383	-0.0232	-0.057	0.1341	0.0469	0.037	-0.0797	-0.0485	0.2917	0.127	0.1284	32.7092	-39.2616	-23.9655
6	0.3719	0.0225	-0.058	0.3005	-0.0383	0.0214	0.0052	-0.0511	-0.0963	-0.0408	-0.0317	-0.0626	-0.0004	0.0431	0.0265	0.0167	0.0025	0.0095	0.1615	0.0502	0.1953	32.8225	-43.9118	-47.2701

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	4 - 402
2	X-RAY DIFFRACTION	2	B	3 - 402
3	X-RAY DIFFRACTION	3	E	2 - 402
4	X-RAY DIFFRACTION	4	F	3 - 402
5	X-RAY DIFFRACTION	5	G	3 - 402
6	X-RAY DIFFRACTION	6	H	4 - 402

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