SAXSdb — 9y6b

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Serine hydroxymethyltransferase

Glycine max

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–471 Chain B； UniProt 1–471 Chain C； UniProt 1–471 Chain D； UniProt 1–471	Mutation：A149T	PLG N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE] × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Ammonium phosphate dibasic 20% w/v Polyethylene glycol 3,350	Resolution 1.90 Å R-free 0.319

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9Y6B	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
10NM CRYO-EM STRUCTURE OF THE A149T DIMER VARIANT OF SERINE HYDROXYMETHYLTRANSFERASE 8 FROM SOYBEAN CULTIVAR ESSEX IN COMPLEX WITH PLP Deposited 2026-01-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–471（471 aa） Chain B 1–471（471 aa）	Mutation：A149T Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：A149T Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；50mM HEPES, 150mM NaCl, 0.5mM TCEP cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.92 Å
6UXH Structure of serine hydroxymethyltransferase 8 from Glycine max cultivar Essex complexed with PLP Deposited 2019-11-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–471（471 aa） Chain B 1–471（471 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.175 M trimethylamine N-oxide, 0.1 M Tris (pH 8.5), 19.5% (w/v) PEG MME 2000	Resolution 1.86 Å R-free 0.231
6UXI Structure of serine hydroxymethyltransferase 8 from Glycine max cultivar Essex complexed with PLP-Glycine Deposited 2019-11-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–471（471 aa） Chain B 1–471（471 aa）	Not recorded	PLG N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE] × 4 EDO 1,2-ETHANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.19 M trimethylamine N-oxide, 0.1 M Tris (pH 8.5), 21% (w/v) PEG MME 2000, 20 mM glycine	Resolution 2.10 Å R-free 0.223
6UXJ Structure of serine hydroxymethyltransferase 8 from Glycine max cultivar Essex complexed with PLP-glycine and 5-formyltetrahydrofolate Deposited 2019-11-07	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–471（471 aa） Chain B 1–471（471 aa） Chain C 1–471（471 aa） Chain D 1–471（471 aa）	Not recorded	PLG N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE] × 4 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 × 4 EDO 1,2-ETHANEDIOL × 17	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.24 M trimethylamine N-oxide, 0.1 M Tris (pH 8.5), 20% (w/v) PEG MME 2000, 10 mM 5-formyl tetrahydrofolate, 20 mM glycine	Resolution 1.40 Å R-free 0.194
9YBZ CRYSTAL STRUCTURE OF THE A149T VARIANT OF SERINE HYDROXYMETHYLTRANSFERASE 8 FROM SOYBEAN CULTIVAR ESSEX IN COMPLEX WITH PLP Deposited 2025-09-17	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–471（471 aa） Chain B 1–471（471 aa） Chain C 1–471（471 aa） Chain D 1–471（471 aa）	Mutation：A149T Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：A149T Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：A149T Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：A149T Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Ammonium tartrate dibasic pH 7.0 12% w/v Polyethylene glycol 3,350	Resolution 2.28 Å R-free 0.313
9YBZ CRYSTAL STRUCTURE OF THE A149T VARIANT OF SERINE HYDROXYMETHYLTRANSFERASE 8 FROM SOYBEAN CULTIVAR ESSEX IN COMPLEX WITH PLP Deposited 2025-09-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain E 1–471（471 aa） Chain F 1–471（471 aa）	Mutation：A149T Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：A149T Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Ammonium tartrate dibasic pH 7.0 12% w/v Polyethylene glycol 3,350	Resolution 2.28 Å R-free 0.313

5 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	K4FZF8_SOYBN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 26–496； UniProt 1–471 Author chain B； PDBConstruct 26–496； UniProt 1–471 Author chain C； PDBConstruct 26–496； UniProt 1–471 Author chain D； PDBConstruct 26–496； UniProt 1–471 Author chain E； PDBConstruct 26–496； UniProt 1–471

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9y6b
Deposition date deposition_date	2025-09-08
Structure title title	CRYSTAL STRUCTURE OF A149T VARIANT OF SERINE HYDROXYMETHYLTRANSFERASE 8 FROM SOYBEAN CULTIVAR ESSEX IN COMPLEX WITH PLP-GLYCINE
Keywords keywords	enzyme, missense variant, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	47.98 Å
Radius of gyration Rg (electron density) rg_electron	48.48 Å
Forward intensity I(0) i0	893572000.00
Molecular weight molecular_weight	245140.0 kDa
Excluded volume excluded_volume	305270 Å³
Envelope volume envelope_volume	394730 Å³
Hydration-shell volume shell_volume	70906 Å³
Envelope diameter envelope_diameter	189.6 Å
Shell Rg shell_rg	48.69 Å
Envelope Rg envelope_rg	49.16 Å
Shape Rg shape_rg	48.48 Å
Total Rg total_rg	48.51 Å
Total atoms total_atoms	17282
Residues n_residues	2299
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	176.9 Å
Rg (real space) rg_real	48.58 Å
Rg uncertainty (real space) rg_real_error	2.20 Å
I(0) (real space) i0_real	8.9360e+08
I(0) uncertainty (real space) i0_real_error	1.7000e+07
Rg (reciprocal space) rg_reciprocal	47.98 Å
I(0) (reciprocal space) i0_reciprocal	892900000.0000
Solution quality estimate total_estimate	0.8086
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	48.3 Å
Skewness Skewness skewness	0.619
Kurtosis Kurtosis kurtosis	-0.074
Angular range angular_range	— – 0.1650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	116600000.0000
Real-space data points n_real_points	34
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.625; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.820; Smooth: 0.812

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Serine hydroxymethyltransferase
Molecular weight formula_weight	54723.0 kDa
EC 编号 ec_number	2.1.2.1
Mutation mutation	A149T
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E
Atom count atom_count	17910

MGMHHHHHHSSGVDLGTENLYFQSNMDPVSVWGNTPLATVDPEIHDLIEKEKRRQCRGIELIASENFTSFAVIEALGSALTNKYSEGMPGNRYYGGNEYIDQIENLCRSRALQAFHLDAQSWGVNVQPYSGSPANFAAYTAVLNPHDRIMGLDLPSGGHLTHGYYTSGGKKISTTSIYFESLPYKVNSTTGYIDYDRLEEKALDFRPKLIICGGSAYPRDWDYKRFREVADKCGALLLCDMAHTSGLVAAQEVNSPFEYCDIVTTTTHKSLRGPRAGMIFYRKGPKPPKKGQPENAVYDFEDKINFAVFPSLQGGPHNHQIGALAVALKQAASPGFKAYAKQVKANAVALGKYLMGKGYSLVTGGTENHLVLWDLRPLGLTGNKVEKLCDLCNITVNKNAVFGDSSALAPGGVRIGAPAMTSRGLVEKDFEQIGEFLHRAVTLTLEIQKEHGKLLKDFNKGLVNNKAIEDLKADVEKFSALFDMPGFLVSEMKYKD

来源 Source

来源生物 organism	Glycine max
通用名 common_name	soybean
NCBI Class编号 ncbi_taxonomy_id	3847
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE]
Molecular weight formula_weight	306.2 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	628

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8. Citations (1)

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Unit-cell length a length_a	174.351 Å
Unit-cell length b length_b	174.351 Å
Unit-cell length c length_c	183.632 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	30

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	trigonal

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	48.540 Å
R factor r_factor	0.2841
R_work r_work	0.2823
R_free r_free	0.3193

fit	/app/data/saxs_computation/y6/9y6b/9y6b.fit
pddf	/app/data/pr_computation/y6/9y6b/9y6b.pr.out
profile	/app/data/saxs_computation/y6/9y6b/9y6b.dat

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

1. Protein Identity and Related Structures Protein Identity & Related Structures

Serine hydroxymethyltransferase

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction