SAXSdb — 5ke1

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

Outer membrane protein IcsA autotransporter

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 419–758	Fragment：UNP residues 419-758	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；0.2 M KCl, 0.1 M TRIS pH 7.2, 26% Jeffamine M-2070	Resolution 1.90 Å R-free 0.195
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 419–758	Fragment：UNP residues 419-758	NI NICKEL (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；0.2 M KCl, 0.1 M TRIS pH 7.2, 26% Jeffamine M-2070	Resolution 1.90 Å R-free 0.195

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 5KE1	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3ML3 Crystal structure of the IcsA autochaperone region Deposited 2010-04-16	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 591–758（168 aa） Fragment：IcsA autochaperone region, UNP residues 591-758	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6；293 K；17% PEG 4000, 10% isopropanol, 0.1M sodium citrate, pH 6.0, EVAPORATION, temperature 293K	Resolution 2.00 Å R-free 0.219

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ICSA_SHIFL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–341； UniProt 419–758 Author chain B； PDBConstruct 2–341； UniProt 419–758

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	5ke1
Deposition date deposition_date	2016-06-09
Structure title title	Structure of a C-terminal fragment of the IcsA/VirG passenger-domain
Keywords keywords	virulence factor, autochaperone, autotransporter, transport protein; TRANSPORT 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	32.06 Å
Radius of gyration Rg (electron density) rg_electron	32.44 Å
Forward intensity I(0) i0	76131200.00
Molecular weight molecular_weight	67890.0 kDa
Excluded volume excluded_volume	84512 Å³
Envelope volume envelope_volume	107570 Å³
Hydration-shell volume shell_volume	30151 Å³
Envelope diameter envelope_diameter	141.1 Å
Shell Rg shell_rg	35.21 Å
Envelope Rg envelope_rg	33.29 Å
Shape Rg shape_rg	32.44 Å
Total Rg total_rg	32.65 Å
Total atoms total_atoms	9464
Residues n_residues	641
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	133.5 Å
Rg (real space) rg_real	32.53 Å
Rg uncertainty (real space) rg_real_error	1.90 Å
I(0) (real space) i0_real	7.6130e+07
I(0) uncertainty (real space) i0_real_error	1.4440e+06
Rg (reciprocal space) rg_reciprocal	32.32 Å
I(0) (reciprocal space) i0_reciprocal	76120000.0000
Solution quality estimate total_estimate	0.7332
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	130.8 Å
Skewness Skewness skewness	0.726
Kurtosis Kurtosis kurtosis	0.515
Angular range angular_range	— – 0.2450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	13060000.0000
Real-space data points n_real_points	50
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.380; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.393; Smooth: 0.994

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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	Outer membrane protein IcsA autotransporter
Molecular weight formula_weight	36601.6 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	9935

GFGNNVKVEAIINNWAQKDYKLLSADKGITGFSVSNISIINPLLTTGAIDYTKSYISDQNKLIYGLSWNDTDGDSHGEFNLKENAELTVSTILADNLSHHNINSWDGKSLTKSGEGTLILAEKNTYSGFTNINAGILKMGTVEAMTRTAGVIVNKGATLNFSGMNQTVNTLLNSGTVLINNINAPFLPDPVIVTGNMTLEKNGHVILNNSSSNVGQTYVQKGNWHGKGGILSLGAVLGNDNSKTDRLEIAGHASGITYVAVTNEGGSGDKTLEGVQIISTDSSDKNAFIQKGRIVAGSYDYRLKQGTVSGLNTNKWYLTSQMDNQESKQMSNQESTQMSSR

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	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	463

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8. Citations (1)

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Unit-cell length a length_a	35.870 Å
Unit-cell length b length_b	84.670 Å
Unit-cell length c length_c	114.270 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	98.46 °
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	1.900 Å
Low-resolution limit resolution_low	42.335 Å
R factor r_factor	0.1679
R_work r_work	0.1664
R_free r_free	0.1950

fit	/app/data/saxs_computation/ke/5ke1/5ke1.fit
pddf	/app/data/pr_computation/ke/5ke1/5ke1.pr.out
profile	/app/data/saxs_computation/ke/5ke1/5ke1.dat

Structure of a C-terminal fragment of the IcsA/VirG passenger-domain

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

Outer membrane protein IcsA autotransporter

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