SAXSdb — 1y7m

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

hypothetical protein BSU14040

Bacillus subtilis subsp. subtilis str. 168

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	CADMIUM ION × 2 SULFATE ION × 4 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O34816_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–164； UniProt 1–164 Author chain B； PDBConstruct 1–164； UniProt 1–164

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	1y7m
Deposition date deposition_date	2004-12-09
Structure title title	Crystal Structure of the B. subtilis YkuD protein at 2 A resolution
Keywords keywords	;surface mutagenesis, cysteine proteases, cell wall catabolism, Structural Genomics, PSI, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, UNKNOWN FUNCTION ;; STRUCTURAL GENOMICS, UNKNOWN FUNCTION
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.

1y7m__assembly_1__model_1

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

Download this curve (.dat)

1y7m__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1y7m__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.59 Å
Rg (electron density)	20.66 Å
Total Rg	21.53 Å
Atom count	2490
Residues	322
Excluded volume	44692 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1y7m__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	hypothetical protein BSU14040
Molecular weight formula_weight	17687.9 kDa
Mutation mutation	K117A, Q118A
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	2646

MLTYQVKQGDTLNSIAADFRISTAALLQANPSLQAGLTAGQSIVIPGLPDPYTIPYHIAVSIGAKTLTLSLNNRVMKTYPIAVGKILTQTPTGEFYIINRQRNPGGPFGAYWLSLSAAHYGIHGTNNPASIGKAVSKGCIRMHNKDVIELASIVPNGTRVTINR

Source Source

Source organism organism	Bacillus subtilis subsp. subtilis str. 168
NCBI taxonomy ID ncbi_taxonomy_id	224308
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	CADMIUM ION
Molecular weight formula_weight	112.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	156

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1y7ma1
Class class	b — All beta proteins
Fold Fold fold	b.160 — L,D-transpeptidase catalytic domain-like
Superfamily Superfamily superfamily	b.160.1 — L,D-transpeptidase catalytic domain-like
Family Family family	b.160.1.1 — L,D-transpeptidase catalytic domain-like

Domain ID domain_id	d1y7ma2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.7 — LysM domain
Superfamily Superfamily superfamily	d.7.1 — LysM domain
Family Family family	d.7.1.1 — LysM domain

Domain ID domain_id	d1y7mb1
Class class	b — All beta proteins
Fold Fold fold	b.160 — L,D-transpeptidase catalytic domain-like
Superfamily Superfamily superfamily	b.160.1 — L,D-transpeptidase catalytic domain-like
Family Family family	b.160.1.1 — L,D-transpeptidase catalytic domain-like

Domain ID domain_id	d1y7mb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.7 — LysM domain
Superfamily Superfamily superfamily	d.7.1 — LysM domain
Family Family family	d.7.1.1 — LysM domain

CATH v4.4 (4 domains)

Domain ID domain_id	1y7mA01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	350 — Membrane-bound Lytic Murein Transglycosylase D; Chain A
Homologous superfamily homologous superfamily	10 — LysM domain

Domain ID domain_id	1y7mA02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	440 — L,D-transpeptidase catalytic domain-like
Homologous superfamily homologous superfamily	10 — L,D-transpeptidase catalytic domain-like

Domain ID domain_id	1y7mB01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	350 — Membrane-bound Lytic Murein Transglycosylase D; Chain A
Homologous superfamily homologous superfamily	10 — LysM domain

Domain ID domain_id	1y7mB02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	440 — L,D-transpeptidase catalytic domain-like
Homologous superfamily homologous superfamily	10 — L,D-transpeptidase catalytic domain-like

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Unit-cell length a length_a	56.276 Å
Unit-cell length b length_b	63.910 Å
Unit-cell length c length_c	93.679 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 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.050 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2140
R_work r_work	0.2110
R_free r_free	0.2700

Crystal Structure of the B. subtilis YkuD protein at 2 A resolution

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

hypothetical protein BSU14040

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

1y7m__assembly_1__model_1

1y7m__assembly_1__model_1 | I(q)

1y7m__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 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 B. subtilis YkuD protein at 2 A resolution

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

hypothetical protein BSU14040

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

1y7m__assembly_1__model_1

1y7m__assembly_1__model_1 | I(q)

1y7m__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)