SAXSdb — 1ysj

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

protein yxeP

Bacillus subtilis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	NICKEL (II) ION × 4 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YXEP_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 25–404； UniProt 1–380 Author chain B； PDBConstruct 25–404； UniProt 1–380

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	1ysj
Deposition date deposition_date	2005-02-08
Structure title title	Crystal Structure of Bacillus Subtilis YXEP Protein (APC1829), a Dinuclear Metal Binding Peptidase from M20 Family
Keywords keywords	;M20 family Peptidase, Dinuclear Metal Binding, Structural Genomics, PSI, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, 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.

1ysj__assembly_1__model_1

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

Download this curve (.dat)

1ysj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1ysj__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	38.26 Å
Rg (electron density)	38.87 Å
Total Rg	38.94 Å
Atom count	5543
Residues	699
Excluded volume	98679 Å³
Maximum q	0.500 Å⁻¹

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

Entity 1 Entity 1 polymer

Description description	protein yxeP
Molecular weight formula_weight	44842.0 kDa
EC 编号 ec_number	3.5.1.14
Mutation mutation	A54G
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	5962

MHHHHHHSSGVDLGTENLYFQSNAMADKAFHTRLINMRRDLHEHPELSFQEVETTKKIRRWLEEEQIEILDVPQLKTGVIAEIKGREDGPVIAIRADIDALPIQEQTNLPFASKVDGTMHACGHDFHTASIIGTAMLLNQRRAELKGTVRFIFQPAEEIAAGARKVLEAGVLNGVSAIFGMHNKPDLPVGTIGVKEGPLMASVDRFEIVIKGKGGHASIPNNSIDPIAAAGQIISGLQSVVSRNISSLQNAVVSITRVQAGTSWNVIPDQAEMEGTVRTFQKEARQAVPEHMRRVAEGIAAGYGAQAEFKWFPYLPSVQNDGTFLNAASEAAARLGYQTVHAEQSPGGEDFALYQEKIPGFFVWMGTNGTEEWHHPAFTLDEEALTVASQYFAELAVIVLETIK

Source Source

Source organism organism	Bacillus subtilis
NCBI taxonomy ID ncbi_taxonomy_id	1423
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	312

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1ysja1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.5 — Zn-dependent exopeptidases
Family Family family	c.56.5.4 — Bacterial dinuclear zinc exopeptidases

Domain ID domain_id	d1ysja2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.19 — Bacterial exopeptidase dimerisation domain
Family Family family	d.58.19.1 — Bacterial exopeptidase dimerisation domain

Domain ID domain_id	d1ysjb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.5 — Zn-dependent exopeptidases
Family Family family	c.56.5.4 — Bacterial dinuclear zinc exopeptidases

Domain ID domain_id	d1ysjb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.19 — Bacterial exopeptidase dimerisation domain
Family Family family	d.58.19.1 — Bacterial exopeptidase dimerisation domain

CATH v4.4 (4 domains)

Domain ID domain_id	1ysjA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	10 — Zn peptidases

Domain ID domain_id	1ysjA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	360 —

Domain ID domain_id	1ysjB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	10 — Zn peptidases

Domain ID domain_id	1ysjB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	360 —

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Unit-cell length a length_a	233.854 Å
Unit-cell length b length_b	42.157 Å
Unit-cell length c length_c	75.449 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	106.71 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	0.1850
R_work r_work	0.1817
R_free r_free	0.2471

Crystal Structure of Bacillus Subtilis YXEP Protein (APC1829), a Dinuclear Metal Binding Peptidase from M20 Family

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

protein yxeP

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

1ysj__assembly_1__model_1

1ysj__assembly_1__model_1 | I(q)

1ysj__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 non-polymer

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 Bacillus Subtilis YXEP Protein (APC1829), a Dinuclear Metal Binding Peptidase from M20 Family

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

protein yxeP

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

1ysj__assembly_1__model_1

1ysj__assembly_1__model_1 | I(q)

1ysj__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 non-polymer

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)