PDB-9dhb: STRUCTURE OF SERINE HYDROXYMETHYLTRANSFERASE 5 FROM GLYCINE MAX C...

ID or keywords:

Entry

Database: PDB / ID: 9dhb

Title

STRUCTURE OF SERINE HYDROXYMETHYLTRANSFERASE 5 FROM GLYCINE MAX CULTIVAR ESSEX COMPLEXED WITH PLP-GLYCINE AND 5-FORMYLTETRAHYDROFOLATE

Components

Serine hydroxymethyltransferase

Keywords

TRANSFERASE / FOLATE METABOLISM / METHYLTRANSFERASE / SOYBEAN CYST NEMATODE INFECTION RESISTANCE / CYTOPLASMIC ENZYME / PLANT PROTEIN

Function / homology

Function and homology information

glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / tetrahydrofolate interconversion / methyltransferase activity / pyridoxal phosphate binding / methylation
Similarity search - Function

Biological species

Glycine max (soybean)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.96 Å

Authors

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

Funding support

United States, 2items

Citation

Journal: To Be Published
Title: STRUCTURE OF SERINE HYDROXYMETHYLTRANSFERASE 5 FROM GLYCINE MAX CULTIVAR ESSEX COMPLEXED WITH PLP-GLYCINE AND 5-FORMYLTETRAHYDROFOLATE
Authors: Owuocha, L.F. / Beamer, L.J.

History

Deposition	Sep 3, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 17, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9dhb.cif.gz	905.5 KB	Display	PDBx/mmCIF format
PDB format	pdb9dhb.ent.gz	622.9 KB	Display	PDB format
PDBx/mmJSON format	9dhb.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9dhb_validation.pdf.gz	3.3 MB	Display	wwPDB validaton report
Full document	9dhb_full_validation.pdf.gz	3.4 MB	Display
Data in XML	9dhb_validation.xml.gz	91.8 KB	Display
Data in CIF	9dhb_validation.cif.gz	125.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dh/9dhb ftp://data.pdbj.org/pub/pdb/validation_reports/dh/9dhb	HTTPS FTP

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Related structure data

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

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	60.732, 131.883, 117.412
Angle α, β, γ (deg.)	90.000, 91.019, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

#1: Protein	Serine hydroxymethyltransferase Mass: 54644.789 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Glycine max (soybean) / Gene: 100815417, GLYMA_05G152100 / Production host: Escherichia coli (E. coli) References: UniProt: A0A0R4J3C9, 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.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₂O₇P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-FFO / N-[4-({[(6S)-2-amino-5-formyl-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid / [6S]-5-FORMYL-TETRAHYDROFOLATE / 6S-FOLINIC ACID Mass: 473.439 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₀H₂₃N₇O₇ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1305 / 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: 2.26 Å³/Da / Density % sol: 45.57 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.22 M TRIMETHYLAMINE N-OXIDE, 0.1 M TRIS (PH 8.5), 20% (W/V) PEG MME 2000

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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: Mar 18, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.96→43.96 Å / Num. obs: 130817 / % possible obs: 99 % / Redundancy: 1.6 % / B_iso Wilson estimate: 29.68 Å² / CC_1/2: 0.997 / Net I/σ(I): 9.3
Reflection shell	Resolution: 1.96→1.99 Å / Num. unique obs: 130817 / CC_1/2: 0.997

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Processing

Software

Name	Version	Classification
PHENIX	1.19.2_4158	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.96→41.17 Å / SU ML: 0.2172 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.9369
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2257	6400	4.91 %
R_work	0.1757	123945	-
obs	0.1781	130345	98.63 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 33.79 Å²

Refinement step

Cycle: LAST / Resolution: 1.96→41.17 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14292	0	240	1305	15837

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0077	15330
X-RAY DIFFRACTION	f_angle_d	1.0311	20854
X-RAY DIFFRACTION	f_chiral_restr	0.0545	2242
X-RAY DIFFRACTION	f_plane_restr	0.0082	2727
X-RAY DIFFRACTION	f_dihedral_angle_d	8.5981	2192

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 (%)
1.96-1.98	0.3157	201	0.2639	3951	X-RAY DIFFRACTION	96.67
1.98-2.01	0.2825	233	0.2465	4139	X-RAY DIFFRACTION	99.21
2.01-2.03	0.314	205	0.2449	4216	X-RAY DIFFRACTION	99.68
2.03-2.06	0.2736	221	0.2279	4127	X-RAY DIFFRACTION	99.77
2.06-2.08	0.3026	218	0.2303	4197	X-RAY DIFFRACTION	99.64
2.08-2.11	0.3103	181	0.2295	4186	X-RAY DIFFRACTION	99.68
2.11-2.14	0.2942	241	0.2129	4124	X-RAY DIFFRACTION	99.89
2.14-2.17	0.2952	240	0.2185	4160	X-RAY DIFFRACTION	99.55
2.17-2.21	0.2714	214	0.2012	4130	X-RAY DIFFRACTION	99.63
2.21-2.24	0.277	208	0.2108	4184	X-RAY DIFFRACTION	99.05
2.24-2.28	0.2566	237	0.2023	4069	X-RAY DIFFRACTION	99.45
2.28-2.32	0.2637	257	0.2151	4164	X-RAY DIFFRACTION	99.57
2.32-2.37	0.2435	229	0.2075	4117	X-RAY DIFFRACTION	99.25
2.37-2.42	0.2524	202	0.1924	4214	X-RAY DIFFRACTION	99.39
2.42-2.47	0.2788	222	0.199	4100	X-RAY DIFFRACTION	99.22
2.47-2.53	0.2623	197	0.201	4209	X-RAY DIFFRACTION	99.46
2.53-2.59	0.2858	188	0.1917	4170	X-RAY DIFFRACTION	99.36
2.59-2.66	0.2689	180	0.1943	4174	X-RAY DIFFRACTION	99.07
2.66-2.74	0.2608	217	0.1829	4173	X-RAY DIFFRACTION	99.37
2.74-2.83	0.2399	199	0.198	4139	X-RAY DIFFRACTION	99.4
2.83-2.93	0.2271	201	0.1901	4184	X-RAY DIFFRACTION	98.87
2.93-3.04	0.2496	226	0.1864	4131	X-RAY DIFFRACTION	98.11
3.04-3.18	0.2472	219	0.1877	4077	X-RAY DIFFRACTION	97.97
3.18-3.35	0.2091	212	0.181	4080	X-RAY DIFFRACTION	97.41
3.35-3.56	0.223	226	0.1732	4054	X-RAY DIFFRACTION	96.37
3.56-3.84	0.2012	219	0.1433	4020	X-RAY DIFFRACTION	96.36
3.84-4.22	0.1735	185	0.1377	4032	X-RAY DIFFRACTION	95.65
4.22-4.83	0.1563	207	0.1275	4112	X-RAY DIFFRACTION	97.27
4.83-6.08	0.1703	222	0.1421	4167	X-RAY DIFFRACTION	98.19
6.08-41.17	0.1873	193	0.1529	4145	X-RAY DIFFRACTION	96.68

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	0.314613244091	0.122652001644	0.0320107927074	0.730488921569	0.223522584034	0.738052209187	-0.0431413787436	0.0504758324844	0.0233573536687	-0.042284020648	-0.00824394537828	-0.00135033358673	-0.0137353006594	-0.0212517343889	-6.45696760173E-5	0.170286321325	-0.0125942885358	0.0120043372788	0.180776633404	-0.0322408718821	0.158201115478	21.4342139925	-24.011504767	4.81549919709
2	0.255467465406	-0.167447301606	-0.183322262831	0.313952644296	0.0144772237135	0.13489579308	0.0180171417135	-0.0242243357317	0.0227042890371	0.10860577977	0.0031330450176	-0.0410776448732	-0.0455463834438	0.0996423868638	-1.86369156291E-5	0.247993410273	-0.0306571262973	0.0176079862617	0.226775828679	-0.0359924136755	0.21810114447	32.8670852393	-21.1210603576	8.39191962161
3	0.305083162717	0.0887337388325	0.349802645615	0.665828547146	0.50710924809	0.950146303445	-0.0300673010468	-0.0119018065061	0.0745807322325	-0.237135191165	-0.144544136896	0.172332514076	0.0627327395081	-0.208341224857	-0.241800854384	0.195701128642	-0.0160119551993	-0.0338495879474	0.286135214719	-0.0773796112799	0.224817516693	9.64784172277	-22.4811311596	-11.4310291957
4	0.184613921442	-0.0157680819692	-0.148338975111	0.572547140937	0.402986865767	0.756383005827	-0.0341971038799	-0.0100436289048	-0.0631881616794	0.0490573889796	-0.0318373743703	0.103669529654	0.185130434088	-0.113260525773	5.87428249984E-6	0.220960706686	-0.0403584747796	0.0440847941305	0.200321874792	-0.0450255071964	0.237991781676	13.1816214768	-38.9976460436	18.1450776372
5	0.195265538105	-0.0442031246502	0.0803933897467	0.252120230802	-0.288908644968	0.444738761453	-0.00601601339911	0.0217912837084	-0.0421991458206	-0.0932121670487	-0.117118006075	0.407442359944	0.162348654576	-0.275084602218	-0.0264995619551	0.141201862226	-0.0815471089591	0.0858305897599	0.266762583887	-0.116406562284	0.34896964147	1.72479527358	-35.9296609295	21.2484557817
6	0.357818192618	-0.0300766454648	-0.0778719143328	0.838533721927	0.16376146149	0.692042747672	-0.0497043067086	0.00823453361471	-0.17560479195	0.154566400178	0.0218105885405	0.00682250600949	0.288311830276	0.0439059430002	-0.000142633140112	0.376400605121	0.0106534965731	0.0422678328727	0.190147414801	-0.0332427251277	0.276211527197	26.471620139	-54.7287598487	19.369409808
7	0.0596060372558	-0.0285268017047	0.0889174988736	0.733962578596	0.285947237675	0.680456480071	-0.016268643607	0.00554431605255	0.0438608011135	-0.0522067153527	-0.0365614969241	0.0597873111015	-0.149810341086	-0.113538123504	-9.49530054711E-6	0.159716457771	0.0414992029607	-0.0353817947401	0.224077917623	-0.0293056789437	0.197583769005	13.0330195571	8.10871467645	40.0351116402
8	0.205215210397	-0.0227850194898	-0.279377000598	0.0333645160025	0.0580259174533	0.346717531767	-0.0420420848567	0.0311535595653	-0.0572371299311	-0.0309692348648	-0.0978751075282	0.122180162015	-0.0413109177755	-0.223983315936	-2.83592614042E-5	0.188851597052	0.0440206004884	-0.0604342511785	0.295287034509	-0.0703200820181	0.25553795891	1.56798891012	5.26103000382	36.3843869908
9	0.499562130548	0.240046103467	0.0482985144357	0.508839613526	0.137443350849	0.502540306674	-0.0301312496836	-0.00714359440344	0.121456645961	-0.079852444388	-0.0120400653934	-0.0578805635252	-0.209026521571	0.0287335050963	1.63345735014E-6	0.277867398764	0.0236379601722	-0.0194481540755	0.204407976632	-0.010679356725	0.248022128189	26.922689628	23.733008237	39.0402286866
10	0.244014331745	-0.142597334892	-0.0239143639579	0.650004315026	0.0811993145686	0.611010939266	-0.0358226497058	-0.0544709361948	-0.0270956355855	0.0391260793713	-0.00669866338044	-0.00712941756588	0.0326590224421	-0.0189985320491	-1.02439179558E-5	0.128249373191	0.0224467127696	-0.00680551100893	0.19285335217	-0.0107041489235	0.169864801798	20.7026520079	-7.03151348905	53.5424220303
11	0.389067215392	0.175664308861	0.318321915684	0.343204147106	-0.0246758771355	0.253744943765	-0.0222682607397	0.0365587513718	-0.0991340284516	-0.0713323003596	-0.0246999727634	-0.128147785109	0.00539169752506	0.131567703161	-1.70537570193E-6	0.180464715693	0.0291620711312	-0.00305093040804	0.229770260443	0.00980174586481	0.257161116121	31.9779252702	-9.90152545849	50.6508724961
12	0.237769776783	0.0537186947494	-0.153868246032	0.718959755072	0.239290204159	1.1974468096	0.00133496870283	-0.00643887159001	-0.062168469628	0.202541981257	-0.114324415152	0.13997723968	-0.0162977369328	-0.308347207187	-0.0484747455351	0.171833345397	0.0160247296086	0.0231100764248	0.313268721294	-0.0423676370154	0.212768433781	7.669288426	-8.04674796761	69.3110649931

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 'A' and (resid 1 through 230 )	A	A	1 - 230	1 - 230
2	2	chain 'A' and (resid 231 through 283 )	A	A	231 - 283	231 - 283
3	3	chain 'A' and (resid 284 through 470 )	A	A	284 - 469	284 - 469
4	4	chain 'B' and (resid 0 through 230 )	B	G	0 - 230	1 - 231
5	5	chain 'B' and (resid 231 through 283 )	B	G	231 - 283	232 - 284
6	6	chain 'B' and (resid 284 through 471 )	B	G	284 - 471	285 - 472
7	7	chain 'C' and (resid -1 through 230 )	C	M	-1 - 230	1 - 232
8	8	chain 'C' and (resid 231 through 283 )	C	M	231 - 283	233 - 285
9	9	chain 'C' and (resid 284 through 471 )	C	M	284 - 471	286 - 473
10	10	chain 'D' and (resid 1 through 230 )	D	R	1 - 230	1 - 230
11	11	chain 'D' and (resid 231 through 283 )	D	R	231 - 283	231 - 283
12	12	chain 'D' and (resid 284 through 470 )	D	R	284 - 470	284 - 470

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