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6uxh

Structure of serine hydroxymethyltransferase 8 from Glycine max cultivar Essex complexed with PLP

Method: X-RAY DIFFRACTION Dmax: 98.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Serine hydroxymethyltransferase

Glycine max

UniProt K4FZF8

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 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

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 6UXH 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 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
6UXI Structure of serine hydroxymethyltransferase 8 from Glycine max cultivar Essex complexed with PLP-Glycine 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）
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 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）
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
9Y6B CRYSTAL STRUCTURE OF A149T VARIANT OF SERINE HYDROXYMETHYLTRANSFERASE 8 FROM SOYBEAN CULTIVAR ESSEX IN COMPLEX WITH PLP-GLYCINE Deposited 2025-09-08 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）
Chain C 1–471（471 aa）
Chain D 1–471（471 aa）
Mutation：A149T Mutation：A149T Mutation：A149T 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
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 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 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 3–473； UniProt 1–471 Author chain B； PDBConstruct 3–473； 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.

SAXS scattering curve SAXS Profile

SAXS profile for 6uxh

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6uxh
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6uxh
Deposition date deposition_date2019-11-07
Structure title titleStructure of serine hydroxymethyltransferase 8 from Glycine max cultivar Essex complexed with PLP
Keywords keywordsfolate metabolism, methyltransferase, soybean cyst, nematode infection resistance, cytoplasmic enzyme, PLANT PROTEIN, TRANSFERASE; PLANT PROTEIN, TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier28.57 Å
Radius of gyration Rg (electron density) rg_electron27.77 Å
Forward intensity I(0) i0156401000.00
Molecular weight molecular_weight99583.0 kDa
Excluded volume excluded_volume124620 ų
Envelope volume envelope_volume144440 ų
Hydration-shell volume shell_volume41694 ų
Envelope diameter envelope_diameter103.4 Å
Shell Rg shell_rg36.57 Å
Envelope Rg envelope_rg28.06 Å
Shape Rg shape_rg27.77 Å
Total Rg total_rg28.58 Å
Total atoms total_atoms7017
Residues n_residues920
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax98.8 Å
Rg (real space) rg_real28.48 Å
Rg uncertainty (real space) rg_real_error0.68 Å
I(0) (real space) i0_real1.5640e+08
I(0) uncertainty (real space) i0_real_error2.1890e+06
Rg (reciprocal space) rg_reciprocal28.52 Å
I(0) (reciprocal space) i0_reciprocal156400000.0000
Solution quality estimate total_estimate0.7902
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary35.3 Å
Skewness Skewness skewness0.286
Kurtosis Kurtosis kurtosis-0.314
Angular range angular_range— – 0.2800 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha68100000.0000
Real-space data points n_real_points57
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.758; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd6uxha1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.67 — PLP-dependent transferase-like
Superfamily Superfamily superfamilyc.67.1 — PLP-dependent transferases
Family Family familyc.67.1.4 — GABA-aminotransferase-like
Domain ID domain_idd6uxha2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd6uxhb1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.67 — PLP-dependent transferase-like
Superfamily Superfamily superfamilyc.67.1 — PLP-dependent transferases
Family Family familyc.67.1.4 — GABA-aminotransferase-like
Domain ID domain_idd6uxhb2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
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8. Citations (1)

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9. Files and Curves (10)