SAXSdb — 9ynb

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

T6SS effector protein PdpC

Francisella tularensis subsp. novicida (strain U112)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	No other associated polymer	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0Q7I0_FRATN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 49–1372； UniProt 2–1325

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	9ynb
Deposition date deposition_date	2025-10-10
Structure title title	Structure of the T6SS effector protein PdpC
Keywords keywords	Francisella, T6SS, secretion, effector, 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.

9ynb__assembly_1__model_1

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

Download this curve (.dat)

9ynb__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9ynb__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	37.58 Å
Rg (electron density)	37.73 Å
Total Rg	37.98 Å
Atom count	7462
Residues	905
Excluded volume	135240 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9ynb__assembly_1__model_1`	monomeric （1）	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 (1)

Entity 1 Entity 1 polymer

Description description	T6SS effector protein PdpC
Molecular weight formula_weight	161288.7 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	7462

MGSSHHHHHHSSGLVPRGSDYKDHDGDYKDHDIDYKDDDDKENLYFQGNDKYELNIYFEKIELPKTADFNMISKHDIKELRVDANLKKKIHLLQFDEDYLAYMRSLRAIHPSKIAMQKIKSIRNKEDSFIIAIFSLDKIIHKTKFISFGHKTVIFDFKKLWGLVDFVIVHTSNKTWVNHKLTSFMPSITYCNQNIIHLAYHSDFLYIYHTPEFMDDINVDRENRRELVAKIPDPYWVRADTKENKININSEEENIEKDLKKITKLKNFEISANDIFFSKAIKAAPRLQHKNKSKLFNSLAIENNEKIKRDIIDYAISNAWYKNEGLLENLMTFLDALVVRHLYLIAVYSVYEIEIGIKSVKPEYSKLLKAGLLNKDIQNQLIYDQKKISNIIWLGETFHGLDIEEAEDLCELIDQGDINPKINPINPEKLYRAYKENYGNEALSFREYKEKYNFLDNDKLREEHANKLSSILEDPKFRVLSYINAFLCSTKNYLVPYGYLGSNPLTYYNCMLETGKRRTSKEAYFADIRNKLFMVCYLPGFLSSVIADDDFIDWYSNKKENQELLKNSYLNNLYKSKQKYIKDFIDLDIIKLLKQTSSQIKPSYIPVAFRYGAFASTTALIRSNANVSNRMEFELYDSPERLHNQYSEKEEMIMPKSVNNPKDHSIDNGISLFSLNLTNEKEDGLRKVMLKVAQLYNLDFKVGISGNLDQAMTQALILGMATTKKNGDILLDEDQMLYMTYLYCIFMAHSVDHTVDEILMSANTYLLNSEEVKYPIFNIADFFARPVFGLSKDKEFKSLVEKYENSLKPNSKILKENYISRVVTLSEVYEVYEDLNCLYSSLSEGSLYNLLSTHSERHCTLLEQYSRKKKAEIGLVQDGEKIKVVNNYSGYAAINQYQRFVSLGRMYDSGAKYSSSHKKQIEKDFNLYLPDKEQINYLKYNFKDNKFDAVYKNKKSKEKNQSHIVYAKKQNTRYCYGYFNDFFVKNRITTFYKIKDKSGNYLVNLHNEKYSFATPNSDSKIYRVSPELLNNRDDFKRVSKDIIKSYKYISFDKQKEDIVKNFGKNLYHTNYEIWVGLSHQAISCFSVLDNIDTQEAANTFIDALYYVRLMQLYYGKTIPFLWISSEIVRYSSSETHYYIPTEENFENILKIALNNASKPVIERFLIILNIYNSTIDNNALILIRCRLPIILFEYEEQKLKLKALQKCADSYKKNNYKNEINFSAWFESIFHVQNLSLSPNYIGNNILILSLVEELKPKCSEYKKNMINQQITAKANELNFYQLLIRLIEISTYHRILTKSIITNTTSLLYDILNKPEFQTINKLINKLFIYKNKDLNTDKYKAFHTKLITIESTYKKINSLYKSDFFKKISS

Source Source

Source organism organism	Francisella tularensis subsp. novicida (strain U112)
NCBI taxonomy ID ncbi_taxonomy_id	401614
Host organism host_organism	Francisella tularensis subsp. novicida (strain U112)

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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	—

Resolution resolution	3.400 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	3.40 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	322627

Structure of the T6SS effector protein PdpC

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

T6SS effector protein PdpC

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

9ynb__assembly_1__model_1

9ynb__assembly_1__model_1 | I(q)

9ynb__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

7. Citations (1)

Structure of the T6SS effector protein PdpC

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

T6SS effector protein PdpC

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

9ynb__assembly_1__model_1

9ynb__assembly_1__model_1 | I(q)

9ynb__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

7. Citations (1)