SAXSdb — 9x4w

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

Aminotransferase-like protein FGM3

Fusarium graminearum PH-1

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–402 Chain B； UniProt 1–402	Not recorded	EQJ (E)-N~2~-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-arginine × 2 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291.15 K；0.1 M SPG and 25% w/v PEG 1500, pH 9.0	Resolution 1.86 Å R-free 0.204

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 9X4W	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9X4U Crystal structure of Fgm3 in complex with PLP Deposited 2025-10-11	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–402（402 aa） Chain B 1–402（402 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；0.03M Sodium fluoride, 0.03M Sodium bromide, 0.03M Sodium iodide, 0.1 M Sodium HEPES, 0.1 M MOPS (acid), 20% v/v PEG 500 MME, 10% w/v PEG 20000, pH 7.5	Resolution 1.67 Å R-free 0.203
9X4U Crystal structure of Fgm3 in complex with PLP Deposited 2025-10-11	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–402（402 aa） Chain D 1–402（402 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；0.03M Sodium fluoride, 0.03M Sodium bromide, 0.03M Sodium iodide, 0.1 M Sodium HEPES, 0.1 M MOPS (acid), 20% v/v PEG 500 MME, 10% w/v PEG 20000, pH 7.5	Resolution 1.67 Å R-free 0.203
9X4V Crystal structure of Fgm3 in complex with PLP and L-Arg Deposited 2025-10-11	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–402（402 aa） Chain B 1–402（402 aa）	Not recorded	EQJ (E)-N~2~-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-arginine × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；0.1 M PCTP and 25% w/v PEG 1500, pH 8.0	Resolution 1.90 Å R-free 0.182
9X50 Crystal structure of Fgm3 in complex with PLP and L-Ala Deposited 2025-10-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–402（402 aa） Chain B 1–402（402 aa）	Not recorded	GOL GLYCEROL × 2 0JO 2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；0.1 M MES, 6.25 % w/v PEG 2000, 6.25 % w/v PEG 3350, 6.25 % w/v PEG 4000, 6.25 % w/v PEG 5000 MME, pH 6.5	Resolution 2.10 Å R-free 0.187
9X51 Crystal structure of Fgm3 in complex with PLP and 4(S)-OH-L-Arg Deposited 2025-10-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–402（402 aa） Chain B 1–402（402 aa）	Not recorded	GOL GLYCEROL × 4 PLP PYRIDOXAL-5'-PHOSPHATE × 2 WYK (2S,4S)-4-hydroxy-L-arginine × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；7.5% w/v PEG 20000/7.5% v/v PEG 550 MME, 0.1 M Tris, 0.08 M Sodium formate, pH 7.5	Resolution 1.48 Å R-free 0.174
9X5B Crystal structure of Fgm3 in complex with PLP and L-Arg Deposited 2025-10-13	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–402（402 aa） Chain B 1–402（402 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	ARG ARGININE × 2 GOL GLYCEROL × 2 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；0.2 M Sodium acetate trihydrate, 0.1 M Sodium HEPES, 25% w/v PEG 3350, pH 7.5	Resolution 2.18 Å R-free 0.229

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

View Construct and Data Evidence

UniProt name	FGM3_GIBZE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–398； UniProt 1–402 Author chain B； PDBConstruct 1–398； UniProt 1–402

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	9x4w
Deposition date deposition_date	2025-10-11
最后修订 last_revision	2026-05-20
Structure title title	Crystal structure of Fgm3 in complex with PLP and L-Arg
Keywords keywords	PLP, Retro-aldol-like, Cbeta-Cgamma Bond Cleavage, BIOSYNTHETIC PROTEIN; BIOSYNTHETIC PROTEIN
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	27.93 Å
Radius of gyration Rg (electron density) rg_electron	27.00 Å
Forward intensity I(0) i0	117962000.00
Molecular weight molecular_weight	87554.0 kDa
Excluded volume excluded_volume	110220 Å³
Envelope volume envelope_volume	124200 Å³
Hydration-shell volume shell_volume	37431 Å³
Envelope diameter envelope_diameter	94.8 Å
Shell Rg shell_rg	35.50 Å
Envelope Rg envelope_rg	27.25 Å
Shape Rg shape_rg	26.96 Å
Total Rg total_rg	27.92 Å
Total atoms total_atoms	6184
Residues n_residues	791
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	90.1 Å
Rg (real space) rg_real	27.86 Å
Rg uncertainty (real space) rg_real_error	0.49 Å
I(0) (real space) i0_real	1.1800e+08
I(0) uncertainty (real space) i0_real_error	1.7190e+06
Rg (reciprocal space) rg_reciprocal	27.88 Å
I(0) (reciprocal space) i0_reciprocal	118000000.0000
Solution quality estimate total_estimate	0.8939
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	31.6 Å
Skewness Skewness skewness	0.317
Kurtosis Kurtosis kurtosis	-0.378
Angular range angular_range	— – 0.2850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	73210000.0000
Real-space data points n_real_points	58
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.880; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.977

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Aminotransferase-like protein FGM3
Molecular weight formula_weight	44835.4 kDa
EC 编号 ec_number	2.-.-.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	7072

MSSSSFSIENVRSQFPALEKRQIFGDNAGGSQVLGTVAKSITEYLIETNVQLGASYKTSTQSTAIFDNAYKAAAKYINAGIDEIVIGASTTQVFRNLAAALKLQPGDELILTNVDHESNIDPWLHYAALNNATIKWWTPSDLNNPKLDPEQLRSLLTNKTRLVACTHCSNILGTINNIKAIADVVHEIPGALLAVDGVAYAPHRAIDVKELGADFYAFSWYKVYGPHISLLYGSKAAQAQLSSLGHFFNPDGSLMDKLELAAASYELTQAIIPLTAYFGENPKQTWDAIAEHEQKLQTRLIEYLVSKPQITVYGETSTDKAVRVPTVSFTVEGMSSQSVVEAVEAVSHAGIRWGHFFSKRLVGSILGLSDDGVVRVSLVHYNTVEEVDQIIVALEMVLLEHHHHHHHH

来源 Source

来源生物 organism	Fusarium graminearum PH-1
NCBI Class编号 ncbi_taxonomy_id	229533
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	(E)-N~2~-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-arginine
Molecular weight formula_weight	403.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	888

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8. Citations (1)

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Unit-cell length a length_a	69.313 Å
Unit-cell length b length_b	96.849 Å
Unit-cell length c length_c	69.713 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	116.60 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.860 Å
Low-resolution limit resolution_low	61.980 Å
R factor r_factor	0.1681
R_work r_work	0.1669
R_free r_free	0.2042

fit	/app/data/saxs_computation/x4/9x4w/9x4w.fit
pddf	/app/data/pr_computation/x4/9x4w/9x4w.pr.out
profile	/app/data/saxs_computation/x4/9x4w/9x4w.dat

Crystal structure of Fgm3 in complex with PLP and L-Arg

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

Aminotransferase-like protein FGM3

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