SAXSdb — 3lyq

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

IpgB2

Shigella flexneri

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–188	Not recorded	FLC CITRATE ANION × 1 FEO MU-OXO-DIIRON × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；5% (w/w) PEG 3350, 7% isopropanol, 10mM FeCl3, 100mM trisodium citrate/citric acid pH 5.5, 10mM NaCl, vapor diffusion, hanging drop, temperature 277K	Resolution 2.30 Å R-free 0.292
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–188	Not recorded	FLC CITRATE ANION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；5% (w/w) PEG 3350, 7% isopropanol, 10mM FeCl3, 100mM trisodium citrate/citric acid pH 5.5, 10mM NaCl, vapor diffusion, hanging drop, temperature 277K	Resolution 2.30 Å R-free 0.292

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 3LYQ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3LW8 Shigella IpgB2 in complex with human RhoA, GDP and Mg2+ (complex A) Deposited 2010-02-23	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 1–188（188 aa）	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；20% (w/v) PEG 3350, pH 7.5, vapor diffusion, hanging drop, temperature 277K	Resolution 1.85 Å R-free 0.233
3LW8 Shigella IpgB2 in complex with human RhoA, GDP and Mg2+ (complex A) Deposited 2010-02-23	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 1–188（188 aa）	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；20% (w/v) PEG 3350, pH 7.5, vapor diffusion, hanging drop, temperature 277K	Resolution 1.85 Å R-free 0.233
3LW8 Shigella IpgB2 in complex with human RhoA, GDP and Mg2+ (complex A) Deposited 2010-02-23	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–188（188 aa）	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；20% (w/v) PEG 3350, pH 7.5, vapor diffusion, hanging drop, temperature 277K	Resolution 1.85 Å R-free 0.233
3LW8 Shigella IpgB2 in complex with human RhoA, GDP and Mg2+ (complex A) Deposited 2010-02-23	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 1–188（188 aa）	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；20% (w/v) PEG 3350, pH 7.5, vapor diffusion, hanging drop, temperature 277K	Resolution 1.85 Å R-free 0.233
3LWN Shigella IpgB2 in complex with human RhoA, GDP and Mg2+ (complex B) Deposited 2010-02-24	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 1–188（188 aa）	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；20% (w/v) PEG 3350; protein was treated with EDTA prior to crystallization, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.28 Å R-free 0.291
3LWN Shigella IpgB2 in complex with human RhoA, GDP and Mg2+ (complex B) Deposited 2010-02-24	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 1–188（188 aa）	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；20% (w/v) PEG 3350; protein was treated with EDTA prior to crystallization, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.28 Å R-free 0.291
3LXR Shigella IpgB2 in complex with human RhoA and GDP (complex C) Deposited 2010-02-25	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 1–188（188 aa）	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 1 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；20% (w/v) PEG 3350; post-crystallization treatment: EDTA, LiSO4, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.68 Å R-free 0.219

3 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q9AJW7_SHIFL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–192； UniProt 1–188 Author chain B； PDBConstruct 5–192； UniProt 1–188

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	3lyq
Deposition date deposition_date	2010-02-28
Structure title title	Crystal structure of IpgB2 from Shigella flexneri
Keywords keywords	IpgB2, GEF, WxxxE, TTSS effector protein, bacterial GEF, cytoskeleton dynamics, RHOA-BINDING PROTEIN; RHOA-BINDING 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	29.53 Å
Radius of gyration Rg (electron density) rg_electron	29.41 Å
Forward intensity I(0) i0	33124500.00
Molecular weight molecular_weight	43008.0 kDa
Excluded volume excluded_volume	53269 Å³
Envelope volume envelope_volume	74016 Å³
Hydration-shell volume shell_volume	22662 Å³
Envelope diameter envelope_diameter	97.6 Å
Shell Rg shell_rg	34.23 Å
Envelope Rg envelope_rg	29.19 Å
Shape Rg shape_rg	29.44 Å
Total Rg total_rg	29.83 Å
Total atoms total_atoms	3002
Residues n_residues	369
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	97.0 Å
Rg (real space) rg_real	29.74 Å
Rg uncertainty (real space) rg_real_error	0.69 Å
I(0) (real space) i0_real	3.3120e+07
I(0) uncertainty (real space) i0_real_error	4.5220e+05
Rg (reciprocal space) rg_reciprocal	29.65 Å
I(0) (reciprocal space) i0_reciprocal	33120000.0000
Solution quality estimate total_estimate	0.8544
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.0 Å
Skewness Skewness skewness	0.419
Kurtosis Kurtosis kurtosis	-0.651
Angular range angular_range	— – 0.2700 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	4716000.0000
Real-space data points n_real_points	55
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.820; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.752; Smooth: 0.890

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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	IpgB2
Molecular weight formula_weight	21936.0 kDa
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	3117

GAMDMLGTSFNNFGISLSHKRYFSGKVDEIIRCTMGKRIVKISSTKINTSILSSVSEQIGENITDWKNDEKKVYVSRVVNQCIDKFCAEHSRKIGDNLRKQIFKQVEKDYRISLDINAAQSSINHLVSGSSYFKKKMDELCEGMNRSVKNDTTSNVANLISDQFFEKNVQYIDLKKLRGNMSDYITNLESPF

来源 Source

来源生物 organism	Shigella flexneri
NCBI Class编号 ncbi_taxonomy_id	623
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CITRATE ANION
Molecular weight formula_weight	189.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	MU-OXO-DIIRON
Molecular weight formula_weight	127.7 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	106

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3lyqA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	4120 — SopE-like GEF fold
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	3lyqB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	4120 — SopE-like GEF fold
Homologous superfamily homologous superfamily	20 —

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8. Citations (1)

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Unit-cell length a length_a	114.080 Å
Unit-cell length b length_b	114.080 Å
Unit-cell length c length_c	88.770 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 4 21 2
Space-group number int_tables_number	90
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	22.880 Å
R factor r_factor	0.2320
R_work r_work	0.2290
R_free r_free	0.2920

fit	/app/data/saxs_computation/ly/3lyq/3lyq.fit
pddf	/app/data/pr_computation/ly/3lyq/3lyq.pr.out
profile	/app/data/saxs_computation/ly/3lyq/3lyq.dat

Crystal structure of IpgB2 from Shigella flexneri

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

IpgB2

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