PDB-8sse: Methionine synthase, C-terminal fragment, Cobalamin and Reactivat...

ID or keywords:

Entry

Database: PDB / ID: 8sse

Title

Methionine synthase, C-terminal fragment, Cobalamin and Reactivation Domains from Thermus thermophilus HB8

Components

Methionine synthase

Keywords

TRANSFERASE / Methyl transferase / cobalamin-dependent / methionine synthase / cobalamin binding / one-carbon metabolism

Function / homology

Function and homology information

methionine synthase / methionine synthase activity / homocysteine metabolic process / cobalamin binding / tetrahydrofolate metabolic process / methylation / zinc ion binding / cytosol
Similarity search - Function

Biological species

Thermus thermophilus HB8 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.15 Å

Authors

Yamada, K. / Mendoza, J. / Koutmos, M.

Funding support

United States, 1items

Citation

Journal: Nat Commun / Year: 2023
Title: Structure of full-length cobalamin-dependent methionine synthase and cofactor loading captured in crystallo.
Authors: Mendoza, J. / Purchal, M. / Yamada, K. / Koutmos, M.

History

Deposition	May 8, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 11, 2023	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 2023	Group: Database references / Category: citation Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title
Revision 1.2	May 1, 2024	Group: Database references / Category: citation Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8sse.cif.gz	1.6 MB	Display	PDBx/mmCIF format
PDB format	pdb8sse.ent.gz	1 MB	Display	PDB format
PDBx/mmJSON format	8sse.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8sse_validation.pdf.gz	1.9 MB	Display	wwPDB validaton report
Full document	8sse_full_validation.pdf.gz	2 MB	Display
Data in XML	8sse_validation.xml.gz	113.1 KB	Display
Data in CIF	8sse_validation.cif.gz	150 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ss/8sse ftp://data.pdbj.org/pub/pdb/validation_reports/ss/8sse	HTTPS FTP

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Related structure data

Related structure data	8sscC 8ssdC 3bulS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	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: Methionine synthase

B: Methionine synthase

C: Methionine synthase

D: Methionine synthase

E: Methionine synthase

F: Methionine synthase

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	166.135, 95.844, 238.745
Angle α, β, γ (deg.)	90.000, 91.956, 90.000
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: ASP / End label comp-ID: ASP / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 663 - 1185 / Label seq-ID: 1 - 523

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12
7	Local NCS retraints between domains: 13 14
8	Local NCS retraints between domains: 15 16
9	Local NCS retraints between domains: 17 18
10	Local NCS retraints between domains: 19 20
11	Local NCS retraints between domains: 21 22
12	Local NCS retraints between domains: 23 24
13	Local NCS retraints between domains: 25 26
14	Local NCS retraints between domains: 27 28
15	Local NCS retraints between domains: 29 30

#1: Protein	Methionine synthase / 5-methyltetrahydrofolate--homocysteine methyltransferase Mass: 58605.441 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Gene: TTHA0618 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SKM5, methionine synthase
#2: Chemical	ChemComp-B12 / COBALAMIN Mass: 1330.356 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₆₂H₈₉CoN₁₃O₁₄P / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 294 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.7 Å³/Da / Density % sol: 54 %
Crystal grow	Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1 M Bis-Tris Propane, pH 7, 60% v/v Tacismate, pH 7, 5% PEG 300, 10% ethylene glycol, 1.5 mM cyanocobalamin

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 16, 2022 Details: K-B pair of biomorph mirrors for vertical and horizontal focusing
Radiation	Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.033 Å / Relative weight: 1
Reflection	Resolution: 3.15→49.295 Å / Num. obs: 64421 / % possible obs: 98.9 % / Redundancy: 3.5 % / CC_1/2: 0.989 / R_merge(I) obs: 0.192 / R_pim(I) all: 0.121 / R_rim(I) all: 0.228 / Χ²: 0.88 / Net I/σ(I): 4.6
Reflection shell	Resolution: 3.15→3.23 Å / % possible obs: 99.4 % / Redundancy: 3.5 % / R_merge(I) obs: 0.973 / Num. measured all: 15918 / Num. unique obs: 4542 / CC_1/2: 0.583 / R_pim(I) all: 0.609 / R_rim(I) all: 1.152 / Χ²: 0.76 / Net I/σ(I) obs: 1.2

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0411	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3bul

3bul

Resolution: 3.15→49.295 Å / Cor.coef. F_o:F_c: 0.917 / Cor.coef. F_o:F_c free: 0.865 / WR_factor R_free: 0.291 / WR_factor R_work: 0.231 / SU B: 80.383 / SU ML: 0.593 / Average fsc free: 0.9366 / Average fsc work: 0.9604 / Cross valid method: THROUGHOUT / ESU R Free: 0.63
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.3067	3279	5.091 %	RANDOM
R_work	0.2453	61130	-	-
all	0.248	-	-	-
obs	-	64409	98.691 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 82.81 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.308 Å²	-0 Å²	-2.874 Å²
2-	-	-0.296 Å²	0 Å²
3-	-	-	1.796 Å²

Refinement step

Cycle: LAST / Resolution: 3.15→49.295 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	24040	0	546	294	24880

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.012	25213
X-RAY DIFFRACTION	r_bond_other_d	0.005	0.016	24211
X-RAY DIFFRACTION	r_angle_refined_deg	1.929	1.692	34249
X-RAY DIFFRACTION	r_angle_other_deg	1.019	1.598	55590
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.18	5	3020
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	11.121	5	221
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.674	10	4191
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.006	10	1163
X-RAY DIFFRACTION	r_chiral_restr	0.093	0.2	3620
X-RAY DIFFRACTION	r_chiral_restr_other	0.115	0.2	9
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	29343
X-RAY DIFFRACTION	r_gen_planes_other	0.005	0.02	5897
X-RAY DIFFRACTION	r_nbd_refined	0.148	0.2	4125
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.133	0.2	21961
X-RAY DIFFRACTION	r_nbtor_refined	0.148	0.2	11421
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.066	0.2	13269
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.111	0.2	325
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.005	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.127	0.2	65
X-RAY DIFFRACTION	r_nbd_other	0.133	0.2	230
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.162	0.2	13
X-RAY DIFFRACTION	r_mcbond_it	8.37	5.843	12134
X-RAY DIFFRACTION	r_mcbond_other	8.369	5.843	12134
X-RAY DIFFRACTION	r_mcangle_it	13.224	10.523	15136
X-RAY DIFFRACTION	r_mcangle_other	13.224	10.524	15137
X-RAY DIFFRACTION	r_scbond_it	8.404	6.365	13079
X-RAY DIFFRACTION	r_scbond_other	8.404	6.365	13080
X-RAY DIFFRACTION	r_scangle_it	13.54	11.422	19113
X-RAY DIFFRACTION	r_scangle_other	13.54	11.422	19114
X-RAY DIFFRACTION	r_lrange_it	21.943	69.145	105067
X-RAY DIFFRACTION	r_lrange_other	21.946	69.155	105016
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.094	0.05	15927
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.089	0.05	16123
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.094	0.05	15952
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.089	0.05	16087
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.098	0.05	15920
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.096	0.05	15954
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.093	0.05	15944
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.092	0.05	15977
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.098	0.05	15937
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.097	0.05	15964
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.089	0.05	16136
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.097	0.05	15917
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.088	0.05	16048
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.101	0.05	15842
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.096	0.05	15941

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.09396	0.0501
1	2	A	X-RAY DIFFRACTION	Local ncs	0.09396	0.0501
2	3	A	X-RAY DIFFRACTION	Local ncs	0.08905	0.0501
2	4	A	X-RAY DIFFRACTION	Local ncs	0.08905	0.0501
3	5	A	X-RAY DIFFRACTION	Local ncs	0.09424	0.0501
3	6	A	X-RAY DIFFRACTION	Local ncs	0.09424	0.0501
4	7	A	X-RAY DIFFRACTION	Local ncs	0.08888	0.0501
4	8	A	X-RAY DIFFRACTION	Local ncs	0.08888	0.0501
5	9	A	X-RAY DIFFRACTION	Local ncs	0.0979	0.0501
5	10	A	X-RAY DIFFRACTION	Local ncs	0.0979	0.0501
6	11	A	X-RAY DIFFRACTION	Local ncs	0.0959	0.0501
6	12	A	X-RAY DIFFRACTION	Local ncs	0.0959	0.0501
7	13	A	X-RAY DIFFRACTION	Local ncs	0.09309	0.0501
7	14	A	X-RAY DIFFRACTION	Local ncs	0.09309	0.0501
8	15	A	X-RAY DIFFRACTION	Local ncs	0.0916	0.0501
8	16	A	X-RAY DIFFRACTION	Local ncs	0.0916	0.0501
9	17	A	X-RAY DIFFRACTION	Local ncs	0.09814	0.0501
9	18	A	X-RAY DIFFRACTION	Local ncs	0.09814	0.0501
10	19	A	X-RAY DIFFRACTION	Local ncs	0.09687	0.0501
10	20	A	X-RAY DIFFRACTION	Local ncs	0.09687	0.0501
11	21	A	X-RAY DIFFRACTION	Local ncs	0.08867	0.0501
11	22	A	X-RAY DIFFRACTION	Local ncs	0.08867	0.0501
12	23	A	X-RAY DIFFRACTION	Local ncs	0.0969	0.0501
12	24	A	X-RAY DIFFRACTION	Local ncs	0.0969	0.0501
13	25	A	X-RAY DIFFRACTION	Local ncs	0.08806	0.0501
13	26	A	X-RAY DIFFRACTION	Local ncs	0.08806	0.0501
14	27	A	X-RAY DIFFRACTION	Local ncs	0.10121	0.0501
14	28	A	X-RAY DIFFRACTION	Local ncs	0.10121	0.0501
15	29	A	X-RAY DIFFRACTION	Local ncs	0.09592	0.0501
15	30	A	X-RAY DIFFRACTION	Local ncs	0.09592	0.0501

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
3.15-3.232	0.402	263	0.35	4497	0.353	4793	0.881	0.91	99.3115	0.334
3.232-3.32	0.375	248	0.33	4409	0.332	4693	0.908	0.928	99.2329	0.306
3.32-3.415	0.321	241	0.276	4167	0.279	4512	0.927	0.953	97.695	0.25
3.415-3.52	0.312	258	0.281	3968	0.283	4403	0.934	0.951	95.98	0.255
3.52-3.635	0.303	191	0.244	4039	0.246	4238	0.945	0.965	99.8112	0.216
3.635-3.762	0.347	208	0.243	3900	0.248	4126	0.925	0.964	99.5637	0.216
3.762-3.903	0.318	227	0.237	3724	0.241	3987	0.941	0.965	99.0971	0.212
3.903-4.061	0.278	171	0.228	3638	0.23	3834	0.956	0.969	99.3479	0.204
4.061-4.24	0.273	185	0.202	3484	0.206	3690	0.959	0.976	99.4309	0.182
4.24-4.446	0.274	156	0.194	3367	0.198	3552	0.957	0.979	99.1836	0.181
4.446-4.684	0.316	166	0.197	3137	0.203	3340	0.942	0.979	98.8922	0.185
4.684-4.965	0.265	165	0.197	2950	0.201	3190	0.957	0.979	97.6489	0.19
4.965-5.304	0.253	150	0.206	2793	0.209	3040	0.962	0.977	96.8092	0.198
5.304-5.724	0.337	133	0.218	2629	0.224	2770	0.944	0.975	99.7112	0.209
5.724-6.262	0.342	125	0.224	2438	0.229	2568	0.935	0.972	99.8053	0.214
6.262-6.987	0.275	120	0.26	2239	0.261	2368	0.957	0.962	99.6199	0.251
6.987-8.041	0.279	94	0.245	1977	0.247	2099	0.952	0.968	98.666	0.246
8.041-9.783	0.251	71	0.244	1660	0.244	1781	0.97	0.974	97.1926	0.255
9.783-13.571	0.347	70	0.295	1300	0.297	1404	0.918	0.964	97.5783	0.313
13.571-49.295	0.323	37	0.364	814	0.363	857	0.935	0.931	99.2999	0.396

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	0.845	-0.154	-0.111	0.0332	-0.0228	0.4935	-0.1486	-0.1947	-0.0304	0.0282	0.0275	0.0228	0.0506	0.0862	0.1211	0.0425	0.0384	0.1095	0.0526	0.0272	0.6402	-3.445	-26.0471	25.655
2	0.4664	0.0435	-0.1464	0.0153	-0.047	0.2938	-0.1368	0.1354	-0.0161	0.0138	-0.0114	0.0023	0.0793	-0.0851	0.1482	0.3188	-0.033	0.2109	0.2137	-0.0486	0.2168	-0.6099	-18.7028	93.6048
3	0.3575	0.3946	0.027	0.4674	0.1369	0.5176	0.069	-0.1033	0.0398	0.0762	-0.1505	-0.0132	0.0528	-0.1289	0.0815	0.0467	-0.0249	0.1426	0.0643	0.0077	0.6152	26.3328	-65.4716	25.6453
4	0.1578	-0.1858	0.0494	0.2994	-0.1603	0.2577	0.0429	0.0108	-0.0065	-0.0488	-0.1328	0.0071	0.0603	0.0777	0.0899	0.2679	0.0213	0.2123	0.2365	-0.0174	0.2051	-30.4994	-58.4872	93.657
5	0.1398	-0.2376	0.1057	0.451	-0.0709	0.4685	-0.0968	-0.0034	-0.0578	0.1281	0.0257	0.0368	-0.1248	0.0348	0.0711	0.1108	-0.014	0.16	0.0074	-0.0315	0.5674	-22.907	-71.4721	25.6161
6	0.0698	0.1859	0.0676	0.8798	0.0999	0.1985	-0.0988	-0.0357	-0.0346	-0.2032	0.0694	-0.0332	-0.0784	-0.0088	0.0294	0.3995	0.0063	0.2347	0.1517	0.0216	0.1741	18.7186	-64.2011	93.5749

Refinement TLS group

Selection: ALL

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