SAXSdb — 4f20

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

Clumping factor B

Staphylococcus aureus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	peptide from Dermokine × 1 （Q6E0U4） MAGNESIUM ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CLFB_STAAR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 18–363； UniProt 197–542

peptide from Dermokine

OrganismNot specified

UniProt Q6E0U4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Clumping factor B × 1 （Q6GDH2） MAGNESIUM ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DMKN_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain Q； PDBConstruct 2–13； UniProt 251–262

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	4f20
Deposition date deposition_date	2012-05-07
Structure title title	Crystal structures reveal the multi-ligand binding mechanism of the Staphylococcus aureus ClfB
Keywords keywords	Dev-IgG fold, protein-peptide complex, Cell Adhesion, Dermokine, Cell Surface, Cell adhesion-Cytokine complex; CELL ADHESION/CYTOKINE
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.

4f20__assembly_1__model_1

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

Download this curve (.dat)

4f20__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4f20__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.77 Å
Rg (electron density)	23.22 Å
Total Rg	23.97 Å
Atom count	2622
Residues	342
Excluded volume	45929 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4f20__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 (4)

Entity 1 Entity 1 polymer

Description description	Clumping factor B
Molecular weight formula_weight	39875.5 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	2635

MRGSHHHHHHENLYFQGSLAVAEPVVNAADAKGTNVNDKVTASDFKLEKTAFDPNQSGNTFMAANFKVTGQVKSGDYFTAKLPDSVTGNGDVDYSNSNNTMPIADIKSTNGDVVAKATYDILTKTYTFVFTDYVNDKENINGQFSLPLFTDRAKAPKSGTYDANINIADEMFDNKITYNYSSPIAGIDKPNGANISSQIIGVDTASGQNTYKQTVFVNPKQRVLGNTWVYIKGYQDKIEESSGKVSATDTKLRIFEVNDTSKLSDSYYADPNDSNLKEVTGEFKDKISYKYDNVASINFGDINKTYVVLVEGHYDNTGKNLKTQVIQENIDPATGKDYSIFGWNNENVVRYGGGSADGDSAVN

Source Source

Source organism organism	Staphylococcus aureus
NCBI taxonomy ID ncbi_taxonomy_id	282458
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	peptide from Dermokine
Molecular weight formula_weight	1096.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Q

GQSGSSGSGSNGD

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	13

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	4f20A01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1280 —

Domain ID domain_id	4f20A02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1290 —

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Unit-cell length a length_a	70.088 Å
Unit-cell length b length_b	70.088 Å
Unit-cell length c length_c	175.760 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	6

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.502 Å
Low-resolution limit resolution_low	34.368 Å
R factor r_factor	0.2261
R_work r_work	0.2239
R_free r_free	0.2700

Crystal structures reveal the multi-ligand binding mechanism of the Staphylococcus aureus ClfB

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

Clumping factor B

State in the Current Structure

Other States of the Same Protein in the Database

peptide from Dermokine

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

4f20__assembly_1__model_1

4f20__assembly_1__model_1 | I(q)

4f20__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structures reveal the multi-ligand binding mechanism of the Staphylococcus aureus ClfB

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

Clumping factor B

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

peptide from Dermokine

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

4f20__assembly_1__model_1

4f20__assembly_1__model_1 | I(q)

4f20__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)