SAXSdb — 3lum

▼

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

Ulilysin

Methanosarcina acetivorans

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	ZINC ION × 1 CALCIUM ION × 3 GLYCEROL × 1 ARGININE × 1 VALINE × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	ZINC ION × 1 CALCIUM ION × 3 GLYCEROL × 2 ARGININE × 1 VALINE × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	ZINC ION × 1 CALCIUM ION × 2 GLYCEROL × 5 ARGININE × 1 VALINE × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	ZINC ION × 1 CALCIUM ION × 3 GLYCEROL × 1 ARGININE × 1 VALINE × 1 water × 1	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 2 CALCIUM ION × 5 GLYCEROL × 6 ARGININE × 2 VALINE × 2 water × 2	Consistent with protein count
6	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 2 CALCIUM ION × 6 GLYCEROL × 4 ARGININE × 2 VALINE × 2 water × 2	Consistent with protein count
7	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 2 CALCIUM ION × 6 GLYCEROL × 2 ARGININE × 2 VALINE × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ULIL_METAC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–262； UniProt 61–322 Author chain B； PDBConstruct 1–262； UniProt 61–322 Author chain C； PDBConstruct 1–262； UniProt 61–322 Author chain D； PDBConstruct 1–262； UniProt 61–322

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3lum
Deposition date deposition_date	2010-02-18
Structure title title	Structure of ulilysin mutant M290L
Keywords keywords	;metallopeptidase, hydrolase, metal ion binding, calcium ion binding, Calcium, Disulfide bond, Metal-binding, Metalloprotease, Protease, Zinc, Zymogen ;; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

3lum__assembly_1__model_1

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

Download this curve (.dat)

3lum__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3lum__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.13 Å
Rg (electron density)	17.93 Å
Total Rg	18.86 Å
Atom count	2069
Residues	262
Excluded volume	36414 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3lum__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3lum__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3lum__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3lum__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`3lum__assembly_5__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`3lum__assembly_6__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`3lum__assembly_7__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Ulilysin
Molecular weight formula_weight	29016.1 kDa
EC 编号 ec_number	3.4.24.-
Mutation mutation	M290L
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	9759

RMEIVKIPVVVHVVWNEEEENISDAQIQSQIDILNKDFRKLNSDVSQVPSVWSNLIADLGIEFFLATKDPNGNQTTGITRTQTSVTFFTTSDEVKFASSGGEDAWPADRYLNIWVCHVLKSEIGQDILGYAQFPGGPAETDGVVIVDAAFGTTGTALPPFDKGRTATHEIGHWLNLYHIWGDELRFEDPCSRSDEVDDTPNQADPNFGCPSYPHVSCSNGPNGDMFMNYLDYVDDKCMVMFTQGQATRVNACLDGPRSSFLA

Source Source

Source organism organism	Methanosarcina acetivorans
NCBI taxonomy ID ncbi_taxonomy_id	2214
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	11

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 5 Entity 5 non-polymer

Description description	ARGININE
Molecular weight formula_weight	175.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	VALINE
Molecular weight formula_weight	117.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1434

▼

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3lumA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	390 — Collagenase (Catalytic Domain)
Homologous superfamily homologous superfamily	10 — Collagenase (Catalytic Domain)

Domain ID domain_id	3lumB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	390 — Collagenase (Catalytic Domain)
Homologous superfamily homologous superfamily	10 — Collagenase (Catalytic Domain)

Domain ID domain_id	3lumC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	390 — Collagenase (Catalytic Domain)
Homologous superfamily homologous superfamily	10 — Collagenase (Catalytic Domain)

Domain ID domain_id	3lumD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	390 — Collagenase (Catalytic Domain)
Homologous superfamily homologous superfamily	10 — Collagenase (Catalytic Domain)

▶

Unit-cell length a length_a	97.310 Å
Unit-cell length b length_b	174.110 Å
Unit-cell length c length_c	124.690 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	32

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	46.280 Å
R factor r_factor	0.1629
R_work r_work	0.1628
R_free r_free	0.1949

Structure of ulilysin mutant M290L

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

Ulilysin

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

3lum__assembly_1__model_1

3lum__assembly_1__model_1 | I(q)

3lum__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (7)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Structure of ulilysin mutant M290L

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

Ulilysin

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

3lum__assembly_1__model_1

3lum__assembly_1__model_1 | I(q)

3lum__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (7)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)