SAXSdb — 4jmf

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

Exoenzyme T

Pseudomonas aeruginosa

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 28–77	Fragment：UNP residues 28-77	Probable chaperone × 2 （G3XD93） GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6.5；295 K；28% PEGMME 5000, 0.2M ammonium sulphate, pH 6.5, vapour diffusion, temperature 295K, VAPOR DIFFUSION	Resolution 2.10 Å R-free 0.243

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 4JMF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6GNN Exoenzyme T from Pseudomonas aeruginosa in complex with human 14-3-3 protein beta, tetrameric crystal form bound to STO1101 Deposited 2018-05-31	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 235–457（223 aa）	Not recorded	F4W 3-(12-oxidanylidene-7-thia-9,11-diazatricyclo[6.4.0.0^{2,6}]dodeca-1(8),2(6),9-trien-10-yl)propanoic acid × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；12% PEG 6000, 0.1M Citrate	Resolution 3.79 Å R-free 0.385

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

View Construct and Data Evidence

UniProt name	Q9I788_PSEAE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–50； UniProt 28–77

Probable chaperone

Pseudomonas aeruginosa

UniProt G3XD93

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain B； UniProt 1–116 Chain C； UniProt 1–116	Not recorded	Exoenzyme T × 1 （Q9I788） GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6.5；295 K；28% PEGMME 5000, 0.2M ammonium sulphate, pH 6.5, vapour diffusion, temperature 295K, VAPOR DIFFUSION	Resolution 2.10 Å R-free 0.243

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	G3XD93_PSEAE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–116； UniProt 1–116 Author chain C； PDBConstruct 1–116； UniProt 1–116

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	4jmf
Deposition date deposition_date	2013-03-14
Structure title title	Crystal structure of ExoT (residues 28 -77)- SpcS complex from Pseudomonas aeruginosa at 2.1 angstrom
Keywords keywords	Type III secretion system, T3SS, virulent effector, TOXIN-CHAPERONE complex; TOXIN/CHAPERONE
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	20.01 Å
Radius of gyration Rg (electron density) rg_electron	19.03 Å
Forward intensity I(0) i0	18381100.00
Molecular weight molecular_weight	31748.0 kDa
Excluded volume excluded_volume	39494 Å³
Envelope volume envelope_volume	45985 Å³
Hydration-shell volume shell_volume	20097 Å³
Envelope diameter envelope_diameter	63.8 Å
Shell Rg shell_rg	25.37 Å
Envelope Rg envelope_rg	19.31 Å
Shape Rg shape_rg	19.03 Å
Total Rg total_rg	19.92 Å
Total atoms total_atoms	2237
Residues n_residues	282
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	64.0 Å
Rg (real space) rg_real	19.94 Å
Rg uncertainty (real space) rg_real_error	0.35 Å
I(0) (real space) i0_real	1.8380e+07
I(0) uncertainty (real space) i0_real_error	2.3490e+05
Rg (reciprocal space) rg_reciprocal	19.95 Å
I(0) (reciprocal space) i0_reciprocal	18380000.0000
Solution quality estimate total_estimate	0.8877
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.8 Å
Skewness Skewness skewness	0.281
Kurtosis Kurtosis kurtosis	-0.344
Angular range angular_range	— – 0.3950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8676000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.857; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.968

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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	Exoenzyme T
Molecular weight formula_weight	5416.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2371

EARQVATPREAQQLAQRQEAPKGEGLLSRLGAALARPFVAIIEWLGKLLG

来源 Source

来源生物 organism	Pseudomonas aeruginosa
NCBI Class编号 ncbi_taxonomy_id	208964
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Probable chaperone
Molecular weight formula_weight	13171.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,C

MNPLYRAAIHQLFLALDLPTPNDEESVLSLQVGPHLCHLAEHPTDHLLMFTRLEGQGDATANEQNLFSQDPCKPILGRDPESGERLLWNRQPLQLLDRAQIHHQLEQLVAAAEELR

来源 Source

来源生物 organism	Pseudomonas aeruginosa
NCBI Class编号 ncbi_taxonomy_id	208964
宿主生物 host_organism	Escherichia coli

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	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	134

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7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4jmfb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.198 — Secretion chaperone-like
Superfamily Superfamily superfamily	d.198.1 — Type III secretory system chaperone-like
Family Family family	d.198.1.0 — automated matches

Domain ID domain_id	d4jmfc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.198 — Secretion chaperone-like
Superfamily Superfamily superfamily	d.198.1 — Type III secretory system chaperone-like
Family Family family	d.198.1.0 — automated matches

CATH v4.4 (3 domains)

Domain ID domain_id	4jmfA00
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	2690 —

Domain ID domain_id	4jmfB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1460 — Yope Regulator; Chain: A,
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	4jmfC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1460 — Yope Regulator; Chain: A,
Homologous superfamily homologous superfamily	10 —

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8. Citations (1)

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Unit-cell length a length_a	78.322 Å
Unit-cell length b length_b	78.322 Å
Unit-cell length c length_c	194.221 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	—

Resolution resolution	2.099 Å
Low-resolution limit resolution_low	30.482 Å
R factor r_factor	0.2020
R_work r_work	0.1977
R_free r_free	0.2431

fit	/app/data/saxs_computation/jm/4jmf/4jmf.fit
pddf	/app/data/pr_computation/jm/4jmf/4jmf.pr.out
profile	/app/data/saxs_computation/jm/4jmf/4jmf.dat

Crystal structure of ExoT (residues 28 -77)- SpcS complex from Pseudomonas aeruginosa at 2.1 angstrom

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

Exoenzyme T

State in the Current Structure

Other States of the Same Protein in the Database

Probable chaperone

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

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)