SAXSdb — 1xkp

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

Chaperone protein sycN

Yersinia pestis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	putative membrane-bound Yop targeting protein YopN × 1 Chaperone protein yscB × 1 （Q56973） water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SYCN_YERPE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–124； UniProt 1–124

Chaperone protein yscB

Yersinia pestis

UniProt Q56973

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	putative membrane-bound Yop targeting protein YopN × 1 Chaperone protein sycN × 1 （P61380） water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YSCB_YERPE
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–137； UniProt 1–137

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	1xkp
Deposition date deposition_date	2004-09-29
Structure title title	Crystal structure of the virulence factor YopN in complex with its heterodimeric chaperone SycN-YscB
Keywords keywords	YopN, Type III secretion, chaperone, SycN, YscB, MEMBRANE PROTEIN-chaperon COMPLEX; MEMBRANE PROTEIN/chaperon
Experimental Method method	X-RAY DIFFRACTION

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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.

1xkp__assembly_1__model_1

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

Download this curve (.dat)

1xkp__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1xkp__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.50 Å
Rg (electron density)	28.38 Å
Total Rg	28.76 Å
Atom count	3773
Residues	457
Excluded volume	67926 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1xkp__assembly_1__model_1`	trimeric （3）	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 (4)

Entity 1 Entity 1 polymer

Description description	putative membrane-bound Yop targeting protein YopN
Molecular weight formula_weight	27741.4 kDa
Mutation mutation	deleted N-terminal 31 and C-terminal 16 residues
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	3952

XQFRGESVQIVSGTLQSIADMAEEVTFVFSERKELSLDKRKLSDSQARVSDVEEQVNQYLSKVPELEQKQNVSELLSLLSNSPNISLSQLKAYLEGKSEEPSEQFKMLCGLRDALKGRPELAHLSHLVEQALVSMAEEQGETIVLGARITPEAYRESQSGVNPLQPLRDTYRDAVMGYQGIYAIWSDLQKRFPNGDIDSVILFLQKALSADLQSQQSGSGREKLGIVISDLQKLKEFGSVSDQVKG

Source Source

Source organism organism	Yersinia pestis
NCBI taxonomy ID ncbi_taxonomy_id	632
Host organism host_organism	Escherichia coli BL21

Entity 2 Entity 2 polymer

Description description	Chaperone protein sycN
Molecular weight formula_weight	13771.0 kDa
Mutation mutation	P123S
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MSWIEPIISHFCQDLGVPTSSPLSPLIQLEMAQSGTLQLEQHGATLTLWLARSLAWHRCEDAMVKALTLTAAQKSGALPLRAGWLGESQLVLFVSLDERSLTLPLLHQAFEQLLRLQQEVLAPP

Source Source

Source organism organism	Yersinia pestis
NCBI taxonomy ID ncbi_taxonomy_id	632
Host organism host_organism	Escherichia coli BL21

Entity 3 Entity 3 polymer

Description description	Chaperone protein yscB
Molecular weight formula_weight	16392.2 kDa
Mutation mutation	C-terminal His-Tag
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MQNLLKNLAASLGRKPFVADKQGVYRLTIDKHLVMLAPHGSELVLRTPIDAPMLREGNNVNVTLLRSLMQQALAWAKRYPQTLVLDDCGQLVLEARLRLQELDTHGLQEVINKQLALLEHLIPQLTPFSVASRVGWNHHHHHH

Source Source

Source organism organism	Yersinia pestis
NCBI taxonomy ID ncbi_taxonomy_id	632
Host organism host_organism	Escherichia coli BL21

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	179

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1xkpa1
Class class	a — All alpha proteins
Fold Fold fold	a.243 — Type III secretion system domain
Superfamily Superfamily superfamily	a.243.1 — Type III secretion system domain
Family Family family	a.243.1.3 — LcrE-like

Domain ID domain_id	d1xkpb1
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.198.1.1 — Type III secretory system chaperone

Domain ID domain_id	d1xkpc1
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.198.1.1 — Type III secretory system chaperone

CATH v4.4 (3 domains)

Domain ID domain_id	1xkpA01
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	670 —

Domain ID domain_id	1xkpB00
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	1xkpC00
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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Unit-cell length a length_a	60.718 Å
Unit-cell length b length_b	60.718 Å
Unit-cell length c length_c	140.419 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	4

Space group space_group	P 41
Space-group number int_tables_number	76
Crystal system crystal_system	—

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	60.860 Å
R factor r_factor	0.2006
R_work r_work	0.1984
R_free r_free	0.2420

Crystal structure of the virulence factor YopN in complex with its heterodimeric chaperone SycN-YscB

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

Chaperone protein sycN

State in the Current Structure

Other States of the Same Protein in the Database

Chaperone protein yscB

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

1xkp__assembly_1__model_1

1xkp__assembly_1__model_1 | I(q)

1xkp__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (2)

Crystal structure of the virulence factor YopN in complex with its heterodimeric chaperone SycN-YscB

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

Chaperone protein sycN

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Chaperone protein yscB

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

1xkp__assembly_1__model_1

1xkp__assembly_1__model_1 | I(q)

1xkp__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (2)