SAXSdb — 13gn

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

L-erythrulose-1-phosphate isomerase

Brucella abortus 2308

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 3–256 Chain D； UniProt 3–256	Fragment：K3-N256 Mutation：A173D	CL CHLORIDE ION × 2 NA SODIUM ION × 3 1GP SN-GLYCEROL-1-PHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；70 mM MES pH 6.5, 70 mM CaCl2, 14% PEG 1500, 8.4% hexanediol. BrabA.00276.a.B2.PW39519 at 15.2 mg/mL. 20 hour soak in 10 mM glycerol 3-phosphate (D/L mixture), 1GP fit best to the electron density, plate Liu-S-202 E9-F10, Puck: PSL-0208, Cryo: 100 mM MES, pH 6.5, 100 mM CaCl2, 20% PEG 1500, 12% hexanediol	Resolution 1.95 Å R-free 0.216
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 3–256 Chain C； UniProt 3–256	Fragment：K3-N256 Mutation：A173D	CL CHLORIDE ION × 1 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；70 mM MES pH 6.5, 70 mM CaCl2, 14% PEG 1500, 8.4% hexanediol. BrabA.00276.a.B2.PW39519 at 15.2 mg/mL. 20 hour soak in 10 mM glycerol 3-phosphate (D/L mixture), 1GP fit best to the electron density, plate Liu-S-202 E9-F10, Puck: PSL-0208, Cryo: 100 mM MES, pH 6.5, 100 mM CaCl2, 20% PEG 1500, 12% hexanediol	Resolution 1.95 Å R-free 0.216

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 13GN	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
11EF Crystal Structure of L-erythrulose-1-phosphate isomerase from Brucella melitensis (P21 form) Deposited 2026-02-18	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 3–256（254 aa） Chain B 3–256（254 aa）	Mutation：A173D Mutation：A173D	CL CHLORIDE ION × 1 GOL GLYCEROL × 2 PO4 PHOSPHATE ION × 3 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；JCSG+ D12: 40 mM potassium phosphate, 16% PEG 8000, 20% glycerol. BrabA.00276.a.B2.PW39519 at 15.2 mg/mL. plate 20694 D12 drop 1, Puck: PSL-1811, Cryo: JCSG+ D12.	Resolution 2.15 Å R-free 0.218
11EF Crystal Structure of L-erythrulose-1-phosphate isomerase from Brucella melitensis (P21 form) Deposited 2026-02-18	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 3–256（254 aa） Chain D 3–256（254 aa）	Mutation：A173D Mutation：A173D	CL CHLORIDE ION × 1 GOL GLYCEROL × 2 PO4 PHOSPHATE ION × 3 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；JCSG+ D12: 40 mM potassium phosphate, 16% PEG 8000, 20% glycerol. BrabA.00276.a.B2.PW39519 at 15.2 mg/mL. plate 20694 D12 drop 1, Puck: PSL-1811, Cryo: JCSG+ D12.	Resolution 2.15 Å R-free 0.218
11EG Crystal Structure of L-erythrulose-1-phosphate isomerase from Brucella melitensis (P1 form) Deposited 2026-02-18	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 3–256（254 aa） Chain B 3–256（254 aa）	Mutation：A173D Mutation：A173D	CL CHLORIDE ION × 6 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；Berkeley B2: 100 mM HEPES, pH 7.5, 400 mM NaCl, 30% PEG 3350. BrabA.00276.a.B2.PW39519 at 15.2 mg/mL. plate 20692 B2 drop 1, Puck: PSL-2008, Cryo: Berkeley B2.	Resolution 1.60 Å R-free 0.183
11EG Crystal Structure of L-erythrulose-1-phosphate isomerase from Brucella melitensis (P1 form) Deposited 2026-02-18	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 3–256（254 aa） Chain D 3–256（254 aa）	Mutation：A173D Mutation：A173D	CL CHLORIDE ION × 4 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；Berkeley B2: 100 mM HEPES, pH 7.5, 400 mM NaCl, 30% PEG 3350. BrabA.00276.a.B2.PW39519 at 15.2 mg/mL. plate 20692 B2 drop 1, Puck: PSL-2008, Cryo: Berkeley B2.	Resolution 1.60 Å R-free 0.183

2 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ERYH_BRUA2
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 9–262； UniProt 3–256 Author chain B； PDBConstruct 9–262； UniProt 3–256 Author chain C； PDBConstruct 9–262； UniProt 3–256 Author chain D； PDBConstruct 9–262； UniProt 3–256

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	13gn
Deposition date deposition_date	2026-05-05
最后修订 last_revision	2026-05-20
Structure title title	Crystal Structure of L-erythrulose-1-phosphate isomerase from Brucella melitensis in complex with SN-GLYCEROL-1-PHOSPHATE
Keywords keywords	;SSGCID, STRUCTURAL GENOMICS, SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE, L-erythrulose-1-phosphate isomerase, Brucella melitensis, Isomerase ;; ISOMERASE
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	35.14 Å
Radius of gyration Rg (electron density) rg_electron	34.80 Å
Forward intensity I(0) i0	173502000.00
Molecular weight molecular_weight	105470.0 kDa
Excluded volume excluded_volume	131820 Å³
Envelope volume envelope_volume	159100 Å³
Hydration-shell volume shell_volume	39578 Å³
Envelope diameter envelope_diameter	123.9 Å
Shell Rg shell_rg	39.28 Å
Envelope Rg envelope_rg	34.75 Å
Shape Rg shape_rg	34.80 Å
Total Rg total_rg	35.10 Å
Total atoms total_atoms	7410
Residues n_residues	969
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	124.9 Å
Rg (real space) rg_real	35.34 Å
Rg uncertainty (real space) rg_real_error	1.32 Å
I(0) (real space) i0_real	1.7350e+08
I(0) uncertainty (real space) i0_real_error	3.1810e+06
Rg (reciprocal space) rg_reciprocal	35.22 Å
I(0) (reciprocal space) i0_reciprocal	173500000.0000
Solution quality estimate total_estimate	0.8430
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	33.3 Å
Skewness Skewness skewness	0.494
Kurtosis Kurtosis kurtosis	-0.220
Angular range angular_range	— – 0.2250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	59780000.0000
Real-space data points n_real_points	46
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.741; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.841; Smooth: 0.892

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	L-erythrulose-1-phosphate isomerase
Molecular weight formula_weight	28744.6 kDa
EC 编号 ec_number	5.3.1.33
Mutation mutation	A173D
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	8026

MAHHHHHHKFWIGTSWKMNKTLAEARLFAEALKAADAGRSPDIQRFVIPPFTAVREVKEILSGTSVKVGAQNMHWADQGAWTGEISPLMLKDCNLDIVELGHSERREHFGETNETVGLKVEAAVRHGLIPLICIGETLEDRESGRAAAVLEEEVRGALSKLSEAQKQAEILFAYEPVWDIGENGIPASADYADARQAEIIAVAQSVLARRVPCLYGGSVNPGNCEELIACPHIDGLFIGRSAWNVEGYLDILARCATKVQAN

来源 Source

来源生物 organism	Brucella abortus 2308
NCBI Class编号 ncbi_taxonomy_id	359391
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 4 Entity 4 non-polymer

Description description	SN-GLYCEROL-1-PHOSPHATE
Molecular weight formula_weight	172.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	573

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8. Citations (1)

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Unit-cell length a length_a	45.802 Å
Unit-cell length b length_b	49.525 Å
Unit-cell length c length_c	104.793 Å
Unit-cell angle α angle_alpha	92.72 °
Unit-cell angle β angle_beta	96.10 °
Unit-cell angle γ angle_gamma	93.72 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.950 Å
Low-resolution limit resolution_low	45.560 Å
R factor r_factor	0.1650
R_work r_work	0.1622
R_free r_free	0.2163

fit	/app/data/saxs_computation/3g/13gn/13gn.fit
pddf	/app/data/pr_computation/3g/13gn/13gn.pr.out
profile	/app/data/saxs_computation/3g/13gn/13gn.dat

Crystal Structure of L-erythrulose-1-phosphate isomerase from Brucella melitensis in complex with SN-GLYCEROL-1-PHOSPHATE

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

L-erythrulose-1-phosphate isomerase

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