PDB-9y7g: CRYSTAL STRUCTURE OF THE A149T VARIANT OF SERINE HYDROXYMETHYLTRA...

ID or keywords:

Entry

Database: PDB / ID: 9y7g

Title

CRYSTAL STRUCTURE OF THE A149T VARIANT OF SERINE HYDROXYMETHYLTRANSFERASE 8 FROM SOYBEAN CULTIVAR FORREST IN COMPLEX WITH PLP

Components

Serine hydroxymethyltransferase

Keywords

TRANSFERASE / enzyme / missense variant

Function / homology

Function and homology information

glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / : / tetrahydrofolate interconversion / methyltransferase activity / pyridoxal phosphate binding / methylation
Similarity search - Function

Biological species

Glycine max (soybean)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.87 Å

Authors

Beamer, L.J. / Samarakoon, V. / Owuocha, L.F.

Funding support

United States, 1items

Citation

Journal: FEBS J / Year: 2026
Title: Oligomeric defects in soybean serine hydroxymethyltransferase 8: tetramer destabilization by A149T and other variants associated with soybean cyst nematode resistance.
Authors: Vindya Samarakoon / David P Buckley / Luckio F Owuocha / Clarissa L Durie / Melissa G Mitchum / Lesa J Beamer /

Abstract: Serine hydroxymethyltransferase (SHMT) is a conserved enzyme in folate-mediated one-carbon metabolism, where it contributes to nucleotide biosynthesis, methylation capacity, and cellular stress ...

History

Deposition	Sep 10, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 8, 2026	Provider: repository / Type: Initial release
Revision 2.0	May 6, 2026	Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_mod_residue / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.label_seq_id / _atom_site_anisotrop.pdbx_label_seq_id / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _pdbx_modification_feature.label_seq_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_struct_mod_residue.label_seq_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_mon_prot_cis.label_seq_id / _struct_mon_prot_cis.pdbx_label_seq_id_2 / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id
Revision 2.1	May 13, 2026	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/y7/9y7g ftp://data.pdbj.org/pub/pdb/validation_reports/y7/9y7g	HTTPS FTP

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Related structure data

Related structure data	75307C 10nmC 9y6bC 9y6dC 9ybzC 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: Serine hydroxymethyltransferase

B: Serine hydroxymethyltransferase

C: Serine hydroxymethyltransferase

D: Serine hydroxymethyltransferase

E: Serine hydroxymethyltransferase

F: Serine hydroxymethyltransferase

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

1

A: Serine hydroxymethyltransferase

B: Serine hydroxymethyltransferase

C: Serine hydroxymethyltransferase

D: Serine hydroxymethyltransferase

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

2

E: Serine hydroxymethyltransferase

F: Serine hydroxymethyltransferase

E: Serine hydroxymethyltransferase

F: Serine hydroxymethyltransferase

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

Unit cell

Length a, b, c (Å)	175.184, 175.184, 183.569
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	152
Space group name H-M	P3₁21
Space group name Hall	P3₁2"
Symmetry operation	#1: x,y,z #2: -y,x-y,z+1/3 #3: -x+y,-x,z+2/3 #4: x-y,-y,-z+2/3 #5: -x,-x+y,-z+1/3 #6: y,x,-z

#1: Protein	Serine hydroxymethyltransferase Mass: 55060.230 Da / Num. of mol.: 6 / Mutation: A149T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Glycine max (soybean) / Gene: SHMT / Production host: Escherichia coli (E. coli) References: UniProt: K4FW35, glycine hydroxymethyltransferase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1045 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	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: 2.49 Å³/Da / Density % sol: 50.55 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M Sodium acetate trihydrate pH 7.0 12% w/v Polyethylene glycol 3,350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
Detector	Type: RDI CMOS_8M / Detector: CMOS / Date: Oct 17, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.87→48.75 Å / Num. obs: 265645 / % possible obs: 99.6 % / Redundancy: 10.2 % / B_iso Wilson estimate: 25.83 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.207 / R_pim(I) all: 0.067 / R_rim(I) all: 0.218 / Net I/σ(I): 10.1
Reflection shell	Resolution: 1.87→1.89 Å / Redundancy: 10.3 % / R_merge(I) obs: 2.918 / Num. unique obs: 12788 / CC_1/2: 0.323 / R_pim(I) all: 0.938 / R_rim(I) all: 3.067 / % possible all: 97.4

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Processing

Software

Name	Version	Classification
PHENIX	1.21.2_5419	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.87→48.75 Å / SU ML: 0.2628 / Cross valid method: FREE R-VALUE / σ(F): 1 / Phase error: 30.0726
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2523	13252	5.01 %
R_work	0.2172	251386	-
obs	0.219	264638	99.23 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 33.94 Å²

Refinement step

Cycle: LAST / Resolution: 1.87→48.75 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	21085	0	0	1045	22130

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0066	21579
X-RAY DIFFRACTION	f_angle_d	0.8706	29311
X-RAY DIFFRACTION	f_chiral_restr	0.0489	3203
X-RAY DIFFRACTION	f_plane_restr	0.0073	3825
X-RAY DIFFRACTION	f_dihedral_angle_d	14.5351	7627

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 (%)
1.87-1.89	0.3835	458	0.3434	8100	X-RAY DIFFRACTION	96.91
1.89-1.91	0.3667	454	0.3347	8140	X-RAY DIFFRACTION	97.48
1.91-1.94	0.3449	429	0.3258	8252	X-RAY DIFFRACTION	98.07
1.94-1.96	0.3559	419	0.3176	8246	X-RAY DIFFRACTION	98.72
1.96-1.99	0.3496	430	0.3056	8366	X-RAY DIFFRACTION	99.18
1.99-2.01	0.3259	482	0.2992	8342	X-RAY DIFFRACTION	99.72
2.01-2.04	0.3052	460	0.2896	8337	X-RAY DIFFRACTION	99.65
2.04-2.07	0.3463	429	0.2912	8346	X-RAY DIFFRACTION	99.77
2.07-2.11	0.3382	524	0.2908	8311	X-RAY DIFFRACTION	99.72
2.11-2.14	0.3013	447	0.2699	8340	X-RAY DIFFRACTION	99.6
2.14-2.18	0.3069	423	0.2638	8382	X-RAY DIFFRACTION	99.81
2.18-2.22	0.3067	434	0.2582	8399	X-RAY DIFFRACTION	99.65
2.22-2.26	0.2985	459	0.2587	8370	X-RAY DIFFRACTION	99.81
2.26-2.31	0.2858	435	0.2441	8436	X-RAY DIFFRACTION	99.71
2.31-2.36	0.3103	410	0.2446	8364	X-RAY DIFFRACTION	99.7
2.36-2.41	0.2772	441	0.2397	8407	X-RAY DIFFRACTION	99.77
2.41-2.47	0.3095	405	0.2311	8410	X-RAY DIFFRACTION	99.62
2.47-2.54	0.2772	431	0.2304	8446	X-RAY DIFFRACTION	99.73
2.54-2.61	0.2601	436	0.2263	8380	X-RAY DIFFRACTION	99.57
2.61-2.7	0.2828	413	0.2335	8447	X-RAY DIFFRACTION	99.45
2.7-2.79	0.276	442	0.2339	8329	X-RAY DIFFRACTION	99.32
2.79-2.91	0.2702	475	0.2265	8332	X-RAY DIFFRACTION	99.11
2.91-3.04	0.2761	435	0.2251	8407	X-RAY DIFFRACTION	99.14
3.04-3.2	0.2575	452	0.2163	8408	X-RAY DIFFRACTION	99.24
3.2-3.4	0.263	451	0.213	8367	X-RAY DIFFRACTION	98.95
3.4-3.66	0.2146	454	0.1957	8409	X-RAY DIFFRACTION	98.91
3.66-4.03	0.1933	415	0.1694	8434	X-RAY DIFFRACTION	98.82
4.03-4.61	0.1788	432	0.156	8493	X-RAY DIFFRACTION	99.06
4.61-5.81	0.1927	437	0.1664	8575	X-RAY DIFFRACTION	99.61
5.81-48.75	0.1842	440	0.1766	8811	X-RAY DIFFRACTION	99.29

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	0.642891581175	-0.108061507307	-0.736639518147	0.647567029234	-0.0384715958697	0.59098620327	-0.186485425623	0.429563466139	0.821568582131	0.0848804599056	-0.105298074604	-0.305969857387	-1.37497939303E-5	0.0846628034011	-0.35786451219	0.186585560109	0.0121607159698	-0.138057645591	0.0458821510998	0.0339192020526	0.63137573261	14.7534639166	26.479712243	-1.35477804728
2	0.781423826547	-0.210989397659	0.150369220661	0.467956265884	-0.0697515354991	0.493495256669	-0.00121934855147	0.146281066678	-0.0873373364181	0.0564133339997	-0.0694934527362	-0.150269927066	0.0728380049047	0.0274046483561	-1.99910975351E-5	0.192730650802	0.00636700467379	0.0275103188482	0.219061023737	0.00114486299671	0.236546178341	17.4263129841	-3.37431179383	-5.73045567851
3	0.591309771791	-0.201044941024	0.0974222970297	0.514682772314	0.108610673516	0.308250367475	-0.0791935203788	0.143851949154	0.301701244561	0.061371198427	-0.0482405692671	-0.0965159371621	0.0900504441386	0.0517707192433	-3.77219059334E-5	0.196036143791	0.00937581096065	0.00421739309178	0.193145864103	0.0432788254057	0.253031321529	25.1915881129	7.49721508671	-1.0090745572
4	0.67354315461	-0.108254871666	-0.369187490662	0.439067534512	0.526468182909	1.69298259626	-0.324971804068	-0.419141050031	0.69083979341	0.583612643233	0.0825291298654	-0.391236698759	0.20846176709	0.801609285336	-0.93516127713	0.164128400233	-0.013322248671	-0.212592240459	0.153955251632	-0.134802269253	0.517871679481	36.2348469165	14.4947402912	18.1569154503
5	0.615447529576	0.203196453346	0.345780660453	1.06210678192	0.0159181877855	0.215840682158	0.0222280387592	-0.048072302934	-0.167480627398	0.0528439521204	-0.0218592393694	-0.0878414209421	0.0152485865118	-0.0161752352004	-0.000166962033881	0.244244704036	-0.0361202702135	0.0355866634227	0.21545699913	-0.00499489877927	0.2599747628	-7.8152623739	-33.4784766177	5.12991794923
6	0.76432812154	0.31858968028	0.0615785485816	0.632624777717	0.149168309551	0.322857752644	0.018024354663	0.0370867757861	-0.271804957253	-0.0237177119818	0.0528051661132	-0.0967661159874	-0.00729789177005	0.0424003460096	0.000683738243912	0.254309042633	-0.0228896013277	0.0280465762655	0.188264757601	-0.0410651028629	0.328806942533	-2.27238213976	-45.3956899263	-2.23141508502
7	0.967936620528	-0.318915803361	0.1242814592	0.972273220515	-0.0151635172041	0.0615793373936	0.0163105842045	0.0029627912386	-0.107098153654	0.0811535062395	-0.0284108452027	0.0500503666608	0.0362817583768	0.0103624070467	-0.000484058177037	0.169577184477	0.0150600908886	-0.0273485248691	0.187535353754	0.0199210317762	0.161821695733	70.8447322775	39.1259496186	1.5152396224
8	0.752545723523	-0.341950799248	0.0866889006485	0.961220296792	0.116531964176	0.335116067631	-0.039049504382	0.0101730322011	-0.175583260184	0.00490384017548	-0.0170828454598	0.278028780068	0.0342182408714	0.0105896882593	-0.000248206629577	0.167605026472	0.0120317844509	-0.019161619489	0.160801495527	0.0103071132481	0.242051355399	65.6289981741	27.7512618412	-5.73322956051
9	0.296616073637	0.387981506723	-0.168210298929	0.598435855602	-0.275066405598	0.182899402638	0.155347366429	0.137073955605	0.102509285841	-0.152453271555	0.00502178153921	0.567553568519	0.269231773389	0.0316657074944	0.252361311027	0.258603493827	0.0863822499778	-0.247251163771	0.363758417365	-0.110379969622	0.419382550108	52.3610457702	29.6639828794	-20.3695694547
10	0.418213013541	-0.208591332887	-0.0232692183877	0.402643996199	0.0306142920921	0.128595060938	-0.0191092156558	0.0213868662456	-0.140084233118	-0.0460783810156	-0.0626357573371	0.272143251928	-0.00495737492541	-0.0105982589723	-9.39166903313E-6	0.190474630924	0.035330157331	-0.0291097585617	0.229188457334	-0.018143671997	0.312085607567	55.7967557927	48.9260136566	-3.61017641823
11	0.695014712121	-0.22849276362	-0.0511317245453	0.39327620412	0.0597849097829	0.237244669529	0.00618644466287	0.00596477293283	0.24196472888	-0.0110552686063	-0.0356837012759	-0.141477317729	-0.052456609603	0.018934636254	4.51233706262E-6	0.188497478583	0.022910803513	-0.025677786631	0.208176555397	0.05637963186	0.310655495685	78.6043855248	65.5578815718	-8.27673111139
12	0.924435769574	-0.168181796808	-0.0430454846368	0.473069993073	0.143770729569	0.509275395335	-0.00165415155481	-0.027306030876	0.20548733601	-0.0745798593689	-0.0580896908154	0.0806722527386	-0.113715247294	0.0296710608342	-0.000420833933906	0.163445219554	0.0184342278199	-0.036282511826	0.175412616528	0.0129937897607	0.223750208289	65.5453993446	70.827269894	0.81260648058
13	0.269905584985	-0.0148836729461	0.192169686724	0.508040840663	0.105491529129	0.0676060989954	-0.214766915783	-0.247319970751	-0.0238659095968	0.131973730443	0.10286628707	0.397665044593	0.0416336000318	-0.0469414663826	0.00977204534557	0.205700455289	0.0720995997226	0.0414473951367	0.34950959664	-0.049143303745	0.312812628158	53.9559492581	69.0952224416	16.8070675209
14	0.38386388687	-0.0358271435596	-0.0601665314626	0.424965842712	0.366418072893	0.29149501367	-0.00849700554578	0.0525542581803	0.135980500944	-0.0703262609452	0.0241452853311	-0.133185436944	-0.00875650161257	0.0686247690239	-0.000673257616445	0.149758143625	-0.0214953259041	-0.0283110958297	0.213604958635	0.0410136173474	0.204868927552	134.234804811	50.1072641307	-3.96530343997
15	0.723370730752	0.185499474485	0.217348102217	0.415512538398	0.0627613839512	0.327755468033	-0.00395125425797	0.0213349125917	-0.125554798189	-0.019175311689	-0.0156789444017	0.18468325831	-0.000836350291225	-0.0244744826855	-0.00112750203949	0.184040406549	0.00234105841946	-0.0470189859275	0.249939023709	0.00500533646549	0.192856484122	109.956897705	33.5970923421	-10.7207320908
16	0.190046184318	-0.00420489388816	-0.0858872369122	0.227774504616	0.00503588553259	0.200721656946	-0.046239052658	0.0924711314593	0.184289121195	-0.126945772752	0.0652147227773	0.0473491264306	-0.0148822268972	0.0160698355921	0.0600889613914	0.21219770856	-0.00476797011108	-0.0416546263839	0.24277761275	0.0311511607336	0.0960733456747	118.942058099	44.2428435731	-16.5005109478
17	0.436185266949	-0.158697792245	0.293364263351	0.536782163518	0.113987309995	0.411715663041	0.047737462241	-0.0786298768692	-0.174353606043	0.0953916829147	0.00596555058364	-0.0544712403539	0.0677851204708	-0.113133217003	8.41193560884E-6	0.219141613529	0.000769162352788	-0.0371824549393	0.245444456372	0.0337183730422	0.21097904221	129.446178198	21.6183224191	6.32880671754
18	1.00278049413	0.0297877584701	-0.140518566771	0.665081359842	0.282805925199	0.376209576437	-0.0164422298512	-0.0255905438696	0.257200039227	0.0272384735167	-0.018912243888	0.0680544539058	-0.0342983812391	-0.0296697478826	-1.05851957926E-5	0.161016071193	-1.42039325654E-5	-0.0258282421705	0.211427015416	0.000254023103803	0.230305454168	119.07990248	59.2621982175	2.54954930995
19	0.631370948133	-0.030372749117	0.129430681052	0.474322383044	0.110928651763	0.64419252431	-0.0533577823886	-0.0325124307963	0.342765851926	0.0178487123986	-0.0516501501085	-0.0616012357864	-0.13922928601	0.0265274790749	-0.0465083867798	0.13268900097	-0.0155118321168	-0.0524832272754	0.146529077309	0.0621180487821	0.300292445257	126.828057735	70.2881186805	-4.34611217137

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'E' and (resid -1 through 89 )	E	E	-1 - 89	1 - 91
2	2	chain 'E' and (resid 90 through 241 )	E	E	90 - 241	92 - 243
3	3	chain 'E' and (resid 242 through 401 )	E	E	242 - 401	244 - 394
4	4	chain 'E' and (resid 402 through 470 )	E	E	402 - 470	395 - 463
5	5	chain 'F' and (resid 0 through 241 )	F	F	0 - 241	1 - 242
6	6	chain 'F' and (resid 242 through 470 )	F	F	242 - 470	243 - 467
7	7	chain 'A' and (resid -1 through 257 )	A	A	-1 - 257	1 - 259
8	8	chain 'A' and (resid 258 through 426 )	A	A	258 - 426	260 - 420
9	9	chain 'A' and (resid 427 through 470 )	A	A	427 - 470	421 - 464
10	10	chain 'B' and (resid -1 through 89 )	B	B	-1 - 89	1 - 91
11	11	chain 'B' and (resid 90 through 257 )	B	B	90 - 257	92 - 259
12	12	chain 'B' and (resid 258 through 426 )	B	B	258 - 426	260 - 415
13	13	chain 'B' and (resid 427 through 470 )	B	B	427 - 470	416 - 459
14	14	chain 'C' and (resid -1 through 89 )	C	C	-1 - 89	1 - 91
15	15	chain 'C' and (resid 90 through 241 )	C	C	90 - 241	92 - 243
16	16	chain 'C' and (resid 242 through 308 )	C	C	242 - 308	244 - 310
17	17	chain 'C' and (resid 309 through 470 )	C	C	309 - 470	311 - 468
18	18	chain 'D' and (resid 0 through 241 )	D	D	0 - 241	1 - 242
19	19	chain 'D' and (resid 242 through 470 )	D	D	242 - 470	243 - 464

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