SAXSdb — 3dpb

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

Chaperone protein caf1M

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	F1 capsule antigen × 2 （P26948） water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CAF1M_YERPE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–235； UniProt 24–258

F1 capsule antigen

Yersinia pestis

UniProt P26948

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Chaperone protein caf1M × 1 （P26926） water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CAF1_YERPE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–149； UniProt 22–170 Author chain C； PDBConstruct 1–149； UniProt 22–170

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	3dpb
Deposition date deposition_date	2008-07-07
Structure title title	Crystal structure of the complex of the Caf1M chaperone with the mini-fiber of two Caf1 subunits (Caf1:Caf1), carrying the Ala9Val, Ala11Val, and Leu13Val mutations in the Gd donor strand
Keywords keywords	;DONOR STRAND COMPLEMENTATION, FIMBRIAE, CHAPERONE, PROTEIN-PROTEIN COMPLEX, BETA BARREL, Immunoglobulin domain, Periplasm, Plasmid, Capsule, Secreted, CHAPERONE-STRUCTURAL PROTEIN COMPLEX ;; CHAPERONE/STRUCTURAL PROTEIN
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.

3dpb__assembly_1__model_1

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

Download this curve (.dat)

3dpb__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3dpb__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.27 Å
Rg (electron density)	26.66 Å
Total Rg	27.27 Å
Atom count	3576
Residues	473
Excluded volume	63613 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3dpb__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 (3)

Entity 1 Entity 1 polymer

Description description	Chaperone protein caf1M
Molecular weight formula_weight	26329.0 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	3706

AQPDIKFASKEYGVTIGESRIIYPLDAAGVMVSVKNTQDYPVLIQSRIYDENKEKESEDPFVVTPPLFRLDAKQQNSLRIAQAGGVFPRDKESLKWLCVKGIPPKDEDIWVDDATNKQKFNPDKDVGVFVQFAINNCIKLLVRPNELKGTPIQFAENLSWKVDGGKLIAENPSPFYMNIGELTFGGKSIPSHYIPPKSTWAFDLPKGLAGARNVSWRIINDQGGLDRLYSKNVTL

Source Source

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

Entity 2 Entity 2 polymer

Description description	F1 capsule antigen
Molecular weight formula_weight	15617.2 kDa
Mutation mutation	Ala9Val, Ala11Val, Leu13Val
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

ADLTASTTVTVTVVEPARITLTYKEGAPITIMDNGNIDTELLVGTLTLGGYKTGTTSTSVNFTDAAGDPMYLTFTSQDGNNHQFTTKVIGKDSRDFDISPKVNGENLVGDDVVLATGSQDFFVRSIGSKGGKLAAGKYTDAVTVTVSNQ

Source Source

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

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	130

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3dpba1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.11 — PapD-like
Family Family family	b.1.11.1 — Pilus chaperone

Domain ID domain_id	d3dpba2
Class class	b — All beta proteins
Fold Fold fold	b.7 — C2 domain-like
Superfamily Superfamily superfamily	b.7.2 — Periplasmic chaperone C-domain
Family Family family	b.7.2.1 — Periplasmic chaperone C-domain

Domain ID domain_id	d3dpbb_
Class class	b — All beta proteins
Fold Fold fold	b.2 — Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily Superfamily superfamily	b.2.3 — Bacterial adhesins
Family Family family	b.2.3.2 — Pilus subunits

Domain ID domain_id	d3dpbc_
Class class	b — All beta proteins
Fold Fold fold	b.2 — Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily Superfamily superfamily	b.2.3 — Bacterial adhesins
Family Family family	b.2.3.2 — Pilus subunits

CATH v4.4 (4 domains)

Domain ID domain_id	3dpbA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3dpbA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3dpbB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1090 — Fimbrial-type adhesion domain

Domain ID domain_id	3dpbC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1090 — Fimbrial-type adhesion domain

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Unit-cell length a length_a	69.909 Å
Unit-cell length b length_b	179.955 Å
Unit-cell length c length_c	45.620 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	8

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	0.2007
R_work r_work	0.1984
R_free r_free	0.2435

Crystal structure of the complex of the Caf1M chaperone with the mini-fiber of two Caf1 subunits (Caf1:Caf1), carrying the Ala9Val, Ala11Val, and Leu13Val mutations in the Gd donor strand

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

Chaperone protein caf1M

State in the Current Structure

Other States of the Same Protein in the Database

F1 capsule antigen

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

3dpb__assembly_1__model_1

3dpb__assembly_1__model_1 | I(q)

3dpb__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of the complex of the Caf1M chaperone with the mini-fiber of two Caf1 subunits (Caf1:Caf1), carrying the Ala9Val, Ala11Val, and Leu13Val mutations in the Gd donor strand

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

Chaperone protein caf1M

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

F1 capsule antigen

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

3dpb__assembly_1__model_1

3dpb__assembly_1__model_1 | I(q)

3dpb__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)