SAXSdb — 9r8g

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

Toxin VasX N-terminal region domain-containing protein

Pseudomonas putida KT2440

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	DUF4123 domain-containing protein × 1 （Q88JN6）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q88JN7_PSEPK
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–996； UniProt 1–996

DUF4123 domain-containing protein

Pseudomonas putida KT2440

UniProt Q88JN6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Toxin VasX N-terminal region domain-containing protein × 1 （Q88JN7）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q88JN6_PSEPK
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 12–318； UniProt 10–316

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	9r8g
Deposition date deposition_date	2025-05-16
Structure title title	Pseudomonas putida Pore-Forming Toxin Tke5 in complex with its cognate Type VI adaptor protein Tap3
Keywords keywords	Pseudomonas putida T6SS effector, Pore-Forming Toxin, MIX family domain, adaptor protein, TOXIN; TOXIN
Experimental Method method	ELECTRON MICROSCOPY

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9r8g__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9r8g__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9r8g__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	39.33 Å
Rg (electron density)	39.11 Å
Total Rg	39.16 Å
Atom count	8811
Residues	1211
Excluded volume	155130 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9r8g__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Toxin VasX N-terminal region domain-containing protein
Molecular weight formula_weight	109903.4 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	8811

MTNASVSSATSGPACSARVPILPVRYAIVPRTADAPACRYADAGFNLEQGFPTLQHSAYTLRALRPGYVYVFMKGPRGEKLVIHEYVGAGLYKELRYQGLEDYHRRERYLSGQSTGWVWADTCQDTAEEVWIGYSPHLWTNAITARITGSAALRKRHMRQLDMAELVSGNQAPSTQPHVLPVSALQTWVEDFKPTERRMPLTWSSDPVTETLPIGNLHAIARHYPWTQPKVPVVVALADAEGMALDLSLSVSAYQHQLRDLMPAEQLEHTKPAQPPEQERVPACYRLDAEQLSPQSRDFHHRNLVAMLLNKTLESLYPADAPSPELAAFRLGTSRRGPALSPAESHFQALTHEDYSPNGARLAQRLDVDKYRRFLAERDALERRIAALRNLALQASNDHDAWLATAEPQHIDNPYSLAAALACYDRDERTSARGLEISLALLIHPMGQPTPGTEDHDRRFKRLEQWLDQHDSPLYTALAPFNPFKDKADSIGTLFGASDNVIEGLAGRFPAMADITDLTAQSVNTVVLKRLRGQTRWDASHGLRRQVQLAAREANAEKALGLLAARYRITEQAITENPFSQEVQRYLKSGMAQVEEMKALRISGSRTVSIELTTTARAKPNFLGLLTSGGGGGLNAGMLWFNILSLKTAYNSLQKSDAPEYTLGFASSVFGVIGAAAATLVSVRATQKAMMLKWISTAPGMAFGNGIINFLTSNLFARASGYPAIIMGFSSDIFKAIRQWQNGNLISGLYTAAASATTALGSILVLEGSLAIAGTTVLIPFAGWTAAGIALIGATLIGGGLFLYSKAHSRLHSPLELWASRSIFGTRENDGEIRDNIKLDFDKKLPPFRHIHEEIKSWQIEFFSPKALLAPYSEQLGLGALTTHLDINNKWPTPDWATIIHTQVTKQNATLELTILLPEFVVGQSEWSGSLVSQNLDRQTTPLQINPDCHITQAGLLLHYKTDARQIRSATLTINYYANQGLDDDTPSTTTIHLER

Source Source

Source organism organism	Pseudomonas putida KT2440
NCBI taxonomy ID ncbi_taxonomy_id	160488
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	DUF4123 domain-containing protein
Molecular weight formula_weight	35710.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MGSSHHHHHHSMTTLSSPPPRSEDFAHNCRFLLLMTSAIENWAYRPIPQEGELVPAYAPSVLDLINAVSRNTQKAWLWKNSALDDRHEFGPLLVDVADAHELLAHAITTWMPIGGAIALDAEVGLAALADHFTSLVQVVLPDHSVATHHVTPDHLAAWLNALDDDHRKAWLGPVSRLAWRVNWGPAHEWKTHENKPIAARSKSELPLTLQQLELDRLQAGMHEHFVLSLAHEVLAMPPHANHTLADIRLWIETLLPQLTALNFRSEEVAGQFIRLIAGHMWLMSNDKAGKIYTNLEESPQARLRELQALVESKEPAHD

Source Source

Source organism organism	Pseudomonas putida KT2440
NCBI taxonomy ID ncbi_taxonomy_id	160488
Host organism host_organism	Escherichia coli BL21(DE3)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

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

Resolution resolution	2.77 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	381732

Pseudomonas putida Pore-Forming Toxin Tke5 in complex with its cognate Type VI adaptor protein Tap3

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

Toxin VasX N-terminal region domain-containing protein

State in the Current Structure

Other States of the Same Protein in the Database

DUF4123 domain-containing protein

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9r8g__assembly_1__model_1

9r8g__assembly_1__model_1 | I(q)

9r8g__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

7. Citations (1)

Pseudomonas putida Pore-Forming Toxin Tke5 in complex with its cognate Type VI adaptor protein Tap3

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

Toxin VasX N-terminal region domain-containing protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DUF4123 domain-containing protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9r8g__assembly_1__model_1

9r8g__assembly_1__model_1 | I(q)

9r8g__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

7. Citations (1)