SAXSdb — 2x4m

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

COAGULASE/FIBRINOLYSIN

YERSINIA PESTIS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	SULFATE ION × 5 (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 5 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	SULFATE ION × 5 (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 3 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	SULFATE ION × 6 (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 3 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	SULFATE ION × 7 (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 3 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	COLY_YERPE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–292； UniProt 21–312 Author chain B； PDBConstruct 1–292； UniProt 21–312 Author chain C； PDBConstruct 1–292； UniProt 21–312 Author chain D； PDBConstruct 1–292； UniProt 21–312

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	2x4m
Deposition date deposition_date	2010-02-05
Structure title title	Yersinia Pestis Plasminogen Activator Pla
Keywords keywords	OMPTIN, TRANSMEMBRANE, ASPARTYL PROTEASE, CELL OUTER MEMBRANE, PROTEASE, HYDROLASE; HYDROLASE
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.

2x4m__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2x4m__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2x4m__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	22.98 Å
Rg (electron density)	22.26 Å
Total Rg	22.95 Å
Atom count	2321
Residues	291
Excluded volume	40340 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2x4m__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2x4m__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2x4m__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2x4m__assembly_4__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 (4)

Entity 1 Entity 1 polymer

Description description	COAGULASE/FIBRINOLYSIN
Molecular weight formula_weight	32953.9 kDa
EC 编号 ec_number	3.4.23.48
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	9482

ASSQLIPNISPDSFTVAASTGMLSGKSHEMLYDAETGRKISQLDWKIKNVAILKGDISWDPYSFLTLNARGWTSLASGSGNMDDYAWMNENQSEWTDHSSHPATNVNHANEYDLNVKGWLLQDENYKAGITAGYQETRFSWTATGGSYSYNNGAYTGNFPKGVRVIGYNQRFSMPYIGLAGQYRINDFELNALFKFSDWVRAHDNDEHYMRDLTFREKTSGSRYYGTVINAGYYVTPNAKVFAEFTYSKYDEGKGGTQTIDKNSGDSVSIGGDAAGISNKNYTVTAGLQYRFGGGGGG

Source Source

Source organism organism	YERSINIA PESTIS
NCBI taxonomy ID ncbi_taxonomy_id	632
Host organism host_organism	ESCHERICHIA COLI BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	23

Entity 3 Entity 3 non-polymer

Description description	(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
Molecular weight formula_weight	306.4 kDa
Source method src_method	syn
Copy count entity_count	14

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	120

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d2x4ma1
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.4 — Transmembrane beta-barrels
Superfamily Superfamily superfamily	f.4.4 — OMPT-like
Family Family family	f.4.4.0 — automated matches

Domain ID domain_id	d2x4ma2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2x4mb1
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.4 — Transmembrane beta-barrels
Superfamily Superfamily superfamily	f.4.4 — OMPT-like
Family Family family	f.4.4.0 — automated matches

Domain ID domain_id	d2x4mb2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2x4mc1
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.4 — Transmembrane beta-barrels
Superfamily Superfamily superfamily	f.4.4 — OMPT-like
Family Family family	f.4.4.0 — automated matches

Domain ID domain_id	d2x4mc2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2x4md1
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.4 — Transmembrane beta-barrels
Superfamily Superfamily superfamily	f.4.4 — OMPT-like
Family Family family	f.4.4.0 — automated matches

Domain ID domain_id	d2x4md2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id	2x4mA00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	90 — OMPT-like

Domain ID domain_id	2x4mB00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	90 — OMPT-like

Domain ID domain_id	2x4mC00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	90 — OMPT-like

Domain ID domain_id	2x4mD00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	90 — OMPT-like

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Unit-cell length a length_a	69.913 Å
Unit-cell length b length_b	127.824 Å
Unit-cell length c length_c	107.175 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.06 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.550 Å
Low-resolution limit resolution_low	19.930 Å
R factor r_factor	0.1860
R_work r_work	0.1850
R_free r_free	0.2460

Yersinia Pestis Plasminogen Activator Pla

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

COAGULASE/FIBRINOLYSIN

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

2x4m__assembly_3__model_1

2x4m__assembly_3__model_1 | I(q)

2x4m__assembly_3__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (8 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Yersinia Pestis Plasminogen Activator Pla

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

COAGULASE/FIBRINOLYSIN

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

2x4m__assembly_3__model_1

2x4m__assembly_3__model_1 | I(q)

2x4m__assembly_3__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (8 domains)

CATH v4.4 (4 domains)

7. Citations (1)