PDB-9y6b: CRYSTAL STRUCTURE OF A149T VARIANT OF SERINE HYDROXYMETHYLTRANSFE...

ID or keywords:

Entry

Database: PDB / ID: 9y6b

Title

CRYSTAL STRUCTURE OF A149T VARIANT OF SERINE HYDROXYMETHYLTRANSFERASE 8 FROM SOYBEAN CULTIVAR ESSEX IN COMPLEX WITH PLP-GLYCINE

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: 1.9 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 8, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 8, 2026	Provider: repository / Type: Initial release
Revision 2.0	Apr 22, 2026	Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / citation / citation_author / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_mon_prot_cis / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range Item: _atom_site.label_seq_id / _atom_site_anisotrop.pdbx_label_seq_id ..._atom_site.label_seq_id / _atom_site_anisotrop.pdbx_label_seq_id / _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 / _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_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_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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9y6b.cif.gz	1 MB	Display	PDBx/mmCIF format
PDB format	pdb9y6b.ent.gz	712 KB	Display	PDB format
PDBx/mmJSON format	9y6b.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/y6/9y6b ftp://data.pdbj.org/pub/pdb/validation_reports/y6/9y6b	HTTPS FTP

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Related structure data

Related structure data	75307C 10nmC 9y6dC 9y7gC 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

hetero molecules

275 kDa, 5 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

hetero molecules

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)	174.351, 174.351, 183.632
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

Details

The ASU contains 6 chains (A,B,C,D,E,F), where the chains A, B, C and D forms the tetramer in the ASU while chains E and F forms tetramers with their symmetry operators, out of the ASU. This mutant datasets show sever tNCS and always have very poor density for chain F. Hence we have left it out and did not build in the chain.

#1: Protein	Serine hydroxymethyltransferase Mass: 54722.965 Da / Num. of mol.: 5 / 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: K4FZF8, glycine hydroxymethyltransferase
#2: Chemical	ChemComp-PLG / N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE] / N-PYRIDOXYL-GLYCINE-5-MONOPHOSPHATE Mass: 306.209 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₂O₇P / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 628 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.98 Å³/Da / Density % sol: 58.67 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M Ammonium phosphate dibasic 20% 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: May 24, 2025
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.9→48.54 Å / Num. obs: 251695 / % possible obs: 99.34 % / Redundancy: 10.3 % / B_iso Wilson estimate: 29.17 Å² / CC_1/2: 0.999 / Net I/σ(I): 16.5
Reflection shell	Resolution: 1.9→1.92 Å / Redundancy: 10.6 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 12400 / CC_1/2: 0.616 / % possible all: 99.91

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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: 1.9→48.54 Å / SU ML: 0.3216 / Cross valid method: FREE R-VALUE / σ(F): 1.01 / Phase error: 37.0993
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.3193	12710	5.08 %
R_work	0.2823	237703	-
obs	0.2841	250413	99.37 %

Solvent computation

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

Displacement parameters

B_iso mean: 40.15 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→48.54 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	17182	0	100	628	17910

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0066	17677
X-RAY DIFFRACTION	f_angle_d	0.8419	24022
X-RAY DIFFRACTION	f_chiral_restr	0.0477	2630
X-RAY DIFFRACTION	f_plane_restr	0.0067	3145
X-RAY DIFFRACTION	f_dihedral_angle_d	15.055	6200

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 (%)
1.9-1.92	0.4255	397	0.4075	7928	X-RAY DIFFRACTION	99.93
1.92-1.94	0.4271	438	0.3881	7851	X-RAY DIFFRACTION	99.92
1.94-1.97	0.3856	401	0.3646	7923	X-RAY DIFFRACTION	99.98
1.97-1.99	0.4081	461	0.3718	7899	X-RAY DIFFRACTION	99.99
1.99-2.02	0.3889	451	0.3645	7881	X-RAY DIFFRACTION	99.99
2.02-2.05	0.4022	454	0.3457	7887	X-RAY DIFFRACTION	99.93
2.05-2.08	0.365	428	0.3394	7968	X-RAY DIFFRACTION	99.87
2.08-2.11	0.3837	431	0.3338	7863	X-RAY DIFFRACTION	99.82
2.11-2.14	0.345	406	0.3131	7921	X-RAY DIFFRACTION	99.71
2.14-2.17	0.3645	412	0.3218	7921	X-RAY DIFFRACTION	99.93
2.17-2.21	0.3749	454	0.3114	7892	X-RAY DIFFRACTION	99.87
2.21-2.25	0.3395	447	0.3016	7894	X-RAY DIFFRACTION	99.73
2.25-2.3	0.3382	460	0.2975	7796	X-RAY DIFFRACTION	98.36
2.3-2.34	0.3527	403	0.3046	7894	X-RAY DIFFRACTION	99.59
2.34-2.39	0.3438	399	0.29	7899	X-RAY DIFFRACTION	99.59
2.39-2.45	0.3576	438	0.2842	7894	X-RAY DIFFRACTION	99.46
2.45-2.51	0.3323	414	0.2843	7952	X-RAY DIFFRACTION	99.61
2.51-2.58	0.3278	445	0.2791	7894	X-RAY DIFFRACTION	99.42
2.58-2.65	0.3441	370	0.2941	7936	X-RAY DIFFRACTION	99.19
2.65-2.74	0.3215	482	0.2809	7864	X-RAY DIFFRACTION	99.5
2.74-2.84	0.2979	369	0.2832	7908	X-RAY DIFFRACTION	98.83
2.84-2.95	0.3388	408	0.2823	7954	X-RAY DIFFRACTION	99.16
2.95-3.09	0.3316	423	0.2769	7860	X-RAY DIFFRACTION	98.57
3.09-3.25	0.3263	413	0.2823	7883	X-RAY DIFFRACTION	98.53
3.25-3.45	0.3054	402	0.2709	7922	X-RAY DIFFRACTION	98.74
3.45-3.72	0.2902	372	0.2548	7991	X-RAY DIFFRACTION	98.55
3.72-4.09	0.2578	407	0.2416	7957	X-RAY DIFFRACTION	98.97
4.09-4.68	0.2552	457	0.231	7874	X-RAY DIFFRACTION	97.86
4.68-5.9	0.2697	421	0.2516	8108	X-RAY DIFFRACTION	99.56
5.9-48.54	0.351	447	0.3009	8289	X-RAY DIFFRACTION	99.19

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	0.422243218608	0.0935012242834	-0.0261363717236	0.328272344753	0.00246814506936	0.309822440598	-0.132487931794	0.0395792379316	-0.56636566111	-0.122085758832	0.0140442031979	-0.361065919634	0.0677814144959	-0.112754720823	-0.185153388613	0.16474810565	0.0517216736279	0.0977712839712	0.195759912174	0.0446033351604	0.514149081235	111.425882591	-69.2103657357	3.82240544718
2	0.187121092579	-0.00865386928788	0.121814596679	0.525809563592	0.0131349978845	0.0905242966335	-0.109941188508	-0.013103821015	-0.260292508915	0.158943512614	0.00512787108833	-0.45508241845	-0.0590826377302	-0.0854992175909	-0.0736126227292	0.242765850368	0.0282200633948	0.081736254266	0.267856535723	0.0177163718128	0.318343296093	114.925538864	-48.136466306	2.39010568596
3	0.029485567378	-0.0265450612369	0.0268742784301	0.0610771322085	0.0102313908309	0.0556275303638	-0.0664798825238	0.0307810522478	0.0582104926532	0.0913220638308	0.0116856946445	0.0625896616561	0.0240635445507	-0.0980332158721	-0.099200472126	0.235636996366	0.0441881240306	0.0442888355458	0.254469619694	-0.0539713909525	0.100481107475	92.9191441964	-30.5286884212	1.81055620007
4	0.235756643251	-0.166430160026	-0.0150697882996	0.116334153031	0.0100475071146	0.0255779740432	-0.069418894151	-0.0194289967519	0.171145643429	0.136440928322	0.0247548971424	-0.150404343389	-0.0451400404896	-0.0715371760089	-0.0386500246813	0.2451395926	0.0458071717624	0.0186220686693	0.236004549195	-0.00427939663073	0.165849872202	106.902552827	-31.9480694012	1.39949321627
5	0.0679026237719	-0.0744675248093	0.067334302483	0.150114193341	-0.0820552210614	0.0677939558566	0.00305248235422	0.173719705192	0.0916359423503	-0.0520018735423	-0.0734457875892	-0.398170656585	-0.100775433501	-0.102695773139	0.00489856807749	0.270017072385	0.0107323755507	0.107277640562	0.349315528643	0.0501420351552	0.35489547099	112.917185302	-22.6599837677	-18.1206528208
6	0.012472487117	0.0578526172858	0.0292247701428	0.232852700981	0.1203711572	0.0660428444454	-0.0097388068933	0.148362162869	-0.107850704429	0.0767255040936	-0.00941089477336	-0.163340186837	0.0301171941479	-0.00752795794887	0.0769556968735	0.263281527559	0.0149090239292	0.23086080893	0.339800286145	0.105077555107	0.579763340538	127.825067012	-31.5289281355	-14.2604987806
7	0.18382333225	-0.094038661652	0.133264760669	0.0844101696946	-0.051523581809	0.148379484487	-0.137828522832	0.123245199271	-0.334360574718	0.101468631888	-0.0454888793442	0.276588681199	-0.0121084727639	-0.0488943411659	-0.177853588662	0.062269264107	0.128396152861	0.0732833166303	0.163328324728	-0.0463143377222	0.938945739242	-15.7893180489	-25.8663015798	1.5663970553
8	0.171457803369	0.0726135182169	-0.069409698084	0.123560687841	-0.0689589630545	0.151589729832	-0.203291249372	0.0560527967261	0.11366027371	-0.050782207063	0.103908931981	-0.29513922017	-0.0703680818405	0.0974448908792	-0.0919698258741	0.0200133244156	0.126032903234	-0.101719255399	0.134078893073	0.086381504691	0.857843614596	11.4971927589	-13.5165816678	5.4648659169
9	0.267290830574	-0.0581247397388	0.133210210864	0.373035222251	0.0640416999915	0.0798510092565	-0.265011026959	0.000498648742125	-0.179627021099	0.178761634625	0.123914416112	0.0994616855036	-0.0281036229211	0.11003286495	-0.0539873976073	0.0769630523443	0.0414247029609	0.0345805918781	0.209913857694	0.0742493505381	0.697195144609	5.90504137183	-26.1571928935	1.3362645198
10	0.0114424116752	-0.00990263099475	-0.0439269962855	0.0591789012948	0.0116860548495	0.116058136403	-0.0647673432578	-0.0010776284111	-0.21704658281	0.0195360916204	-0.0252159511092	0.089552786559	0.0392780286112	0.157017871889	-0.0425230306593	0.0431020708359	0.0638546570303	0.0531627317691	0.283427372385	-0.153800012075	0.727622325721	4.68570356281	-39.547045091	-16.9899388039
11	0.17617351433	0.231468982306	-0.068590927217	0.331008945685	-0.0847444319952	0.0229456528339	-0.0660920936655	-0.036326721364	0.0962145015869	0.0430733547418	0.0278818395422	0.20365903305	0.0531849592264	-0.00169673616259	-0.0125790686702	0.193215837722	-0.0104318843669	0.0141489015491	0.279540835035	-0.0153786843804	0.158953673691	44.6577895073	-50.3039534385	1.92369843722
12	0.0295587416178	-0.0141789792643	0.0104265845612	0.0184886325411	0.00556711529122	0.0396969638451	0.0234658903777	0.202984958549	-0.393874295681	-0.145304910747	-0.121518509196	-0.0789798493049	0.138265371619	0.00689589877636	-8.25213991677E-6	0.263589310406	0.028543399696	0.058639695179	0.309220732892	-0.0149277773862	0.605171200774	69.5157530062	-67.3989010605	0.588566030558
13	0.0871931075769	-0.0432814327158	-0.102342628666	0.0989374467566	0.0120920021394	0.120062776529	-0.0282332368543	-0.120493767352	-0.372303069845	0.0645046841395	0.0105158343548	-0.0700730976286	-0.0114342247744	0.0617113883064	-0.000595399134265	0.217043534334	0.00657388555452	0.0278587233396	0.295145141439	0.0372565474424	0.357568772452	54.5562331285	-63.1768409225	9.37264397588
14	0.300000171353	-0.240912735019	0.0526009436159	0.230036903553	-0.0336402776088	0.0796242702694	-0.223851499442	0.0539159693548	-0.327272422463	-0.0144209001339	0.0723586061129	0.0369386635647	0.12341408974	-0.111359172495	-0.0199830405721	0.256652527025	-0.0904497992047	0.0846060921653	0.267561980216	-0.130649105931	0.453918647289	44.915427839	-76.4375150749	-13.2919437039
15	0.158689050417	-0.00259406456999	0.0811878712332	0.0713198179999	-0.0569875254394	0.0791681497215	-0.075831072348	0.0296865845957	0.0288136865796	-0.0854818084126	0.116641431076	0.199376105548	0.0432669226655	-0.0545470573643	7.26140961557E-6	0.263306878096	-0.00745178639623	0.011940326534	0.306797388866	-0.0317872615768	0.3205871688	40.69802299	-49.683673981	-3.57609536045
16	0.624936118314	0.132925660168	-0.0921468927941	0.149934721767	-0.0109319364512	0.161858289462	-0.0562360388649	0.115719498293	0.419964360919	-0.111683526347	0.0425450598629	-0.0453085324923	-0.0191755625486	-0.00891173671282	-0.0185789353675	0.218294675616	-0.0141835040715	0.0173947343921	0.310623189452	-0.00759965543045	0.151523271884	59.303622197	-33.0305259702	-8.30972536435
17	0.126844641849	0.16605623104	0.0301803892096	0.338539896033	-0.0488604780082	0.0904260101047	-0.018362888719	-0.149674019558	0.229717341583	0.0849841954894	0.146937656902	0.31689725617	-0.0263623070812	0.0274444292124	0.0500536683734	0.219476048348	0.0523265834179	0.0700470216965	0.354368484211	-0.07421749753	0.460758333368	42.4351503588	-23.7575688262	9.82068380508
18	0.109995031413	-0.079973448467	0.00547729522518	0.14606305828	0.0402055924132	0.0669196591748	-0.109506585243	0.0780095760276	-0.213454511009	-0.0872175329993	0.0606465627118	-0.401107256405	-0.0424819596075	0.0661016734322	0.00339384873664	0.206325519973	0.0367246693846	0.046187712325	0.201136041832	0.0103435628802	0.521768904051	118.9300897	-48.841695161	-2.56314365226
19	0.112410168493	0.0199214578596	0.0907326516019	0.0293051843102	-0.00399345500931	0.33043857038	0.00864416684828	-0.0551831218562	-0.647222504018	0.0187018776066	0.00986836963838	0.0744279759151	-0.00546736514226	-0.0463457591603	-0.0238884812837	0.20531160763	-0.00777060474834	0.110726310801	0.191668751318	-0.0761772913029	0.602855611064	94.4827196373	-66.3442080446	-6.66495776781

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 'C' and (resid 237 through 470 )	C	E	237 - 470	239 - 460
2	2	chain 'D' and (resid -1 through 117 )	D	G	-1 - 117	1 - 119
3	3	chain 'D' and (resid 118 through 241 )	D	G	118 - 241	120 - 243
4	4	chain 'D' and (resid 242 through 367 )	D	G	242 - 367	244 - 367
5	5	chain 'D' and (resid 368 through 440 )	D	G	368 - 440	368 - 434
6	6	chain 'D' and (resid 441 through 470 )	D	G	441 - 470	435 - 464
7	7	chain 'E' and (resid -1 through 89 )	E	I	-1 - 89	1 - 91
8	8	chain 'E' and (resid 90 through 241 )	E	I	90 - 241	92 - 243
9	9	chain 'E' and (resid 242 through 401 )	E	I	242 - 401	244 - 391
10	10	chain 'E' and (resid 402 through 470 )	E	I	402 - 470	392 - 460
11	11	chain 'A' and (resid 0 through 117 )	A	A	0 - 117	1 - 118
12	12	chain 'A' and (resid 118 through 197 )	A	A	118 - 197	119 - 198
13	13	chain 'A' and (resid 198 through 332 )	A	A	198 - 332	199 - 326
14	14	chain 'A' and (resid 333 through 470 )	A	A	333 - 470	327 - 457
15	15	chain 'B' and (resid 0 through 89 )	B	C	0 - 89	1 - 90
16	16	chain 'B' and (resid 90 through 367 )	B	C	90 - 367	91 - 359
17	17	chain 'B' and (resid 368 through 470 )	B	C	368 - 470	360 - 458
18	18	chain 'C' and (resid -1 through 89 )	C	E	-1 - 89	1 - 91
19	19	chain 'C' and (resid 90 through 236 )	C	E	90 - 236	92 - 238

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