SAXSdb — 4mll

▼

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

Beta-lactamase OXA-1

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	(2R,4S)-5,5-dimethyl-2-[(1R)-1-{[(5-methyl-3-phenyl-1,2-oxazol-4-yl)carbonyl]amino}-2-oxoethyl]-1,3-thiazolidine-4-carb oxylic acid × 1 PHOSPHATE ION × 3 (4S)-2-METHYL-2,4-PENTANEDIOL × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	(2R,4S)-5,5-dimethyl-2-[(1R)-1-{[(5-methyl-3-phenyl-1,2-oxazol-4-yl)carbonyl]amino}-2-oxoethyl]-1,3-thiazolidine-4-carb oxylic acid × 1 PHOSPHATE ION × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	(2R,4S)-5,5-dimethyl-2-[(1R)-1-{[(5-methyl-3-phenyl-1,2-oxazol-4-yl)carbonyl]amino}-2-oxoethyl]-1,3-thiazolidine-4-carb oxylic acid × 1 PHOSPHATE ION × 2 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	(2R,4S)-5,5-dimethyl-2-[(1R)-1-{[(5-methyl-3-phenyl-1,2-oxazol-4-yl)carbonyl]amino}-2-oxoethyl]-1,3-thiazolidine-4-carb oxylic acid × 1 PHOSPHATE ION × 1 (4S)-2-METHYL-2,4-PENTANEDIOL × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BLO1_ECOLX
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–251； UniProt 26–276 Author chain B； PDBConstruct 1–251； UniProt 26–276 Author chain C； PDBConstruct 1–251； UniProt 26–276 Author chain D； PDBConstruct 1–251； UniProt 26–276

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	4mll
Deposition date deposition_date	2013-09-06
Structure title title	The 1.4 A structure of the class D beta-lactamase OXA-1 K70D complexed with oxacillin
Keywords keywords	Hydrolase, Oxacillinase, Antibiotic Resistance, HYDROLASE-ANTIBIOTIC complex; HYDROLASE/ANTIBIOTIC
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.

4mll__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4mll__assembly_4__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4mll__assembly_4__model_1 | P(r) · Pending

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

Rg（Guinier）	18.52 Å
Rg (electron density)	17.30 Å
Total Rg	18.35 Å
Atom count	2009
Residues	250
Excluded volume	35844 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4mll__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4mll__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4mll__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`4mll__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Beta-lactamase OXA-1
Molecular weight formula_weight	28146.7 kDa
EC 编号 ec_number	3.5.2.6
Mutation mutation	K70D
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	9318

STDISTVASPLFEGTEGCFLLYDASTNAEIAQFNKAKCATQMAPDSTFDIALSLMAFDAEIIDQKTIFKWDKTPKGMEIWNSNHTPKTWMQFSVVWVSQEITQKIGLNKIKNYLKDFDYGNQDFSGDKERNNGLTEAWLESSLKISPEEQIQFLRKIINHNLPVKNSAIENTIENMYLQDLDNSTKLYGKTGAGFTANRTLQNGWFEGFIISKSGHKYVFVSALTGNLGSNLTSSIKAKKNAITILNTLNL

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	(2R,4S)-5,5-dimethyl-2-[(1R)-1-{[(5-methyl-3-phenyl-1,2-oxazol-4-yl)carbonyl]amino}-2-oxoethyl]-1,3-thiazolidine-4-carb oxylic acid
Molecular weight formula_weight	403.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 4 Entity 4 non-polymer

Description description	(4S)-2-METHYL-2,4-PENTANEDIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	945

▼

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d4mlla_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.3 — beta-lactamase/transpeptidase-like
Superfamily Superfamily superfamily	e.3.1 — beta-lactamase/transpeptidase-like
Family Family family	e.3.1.1 — beta-Lactamase/D-ala carboxypeptidase

Domain ID domain_id	d4mllb_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.3 — beta-lactamase/transpeptidase-like
Superfamily Superfamily superfamily	e.3.1 — beta-lactamase/transpeptidase-like
Family Family family	e.3.1.1 — beta-Lactamase/D-ala carboxypeptidase

Domain ID domain_id	d4mllc_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.3 — beta-lactamase/transpeptidase-like
Superfamily Superfamily superfamily	e.3.1 — beta-lactamase/transpeptidase-like
Family Family family	e.3.1.1 — beta-Lactamase/D-ala carboxypeptidase

Domain ID domain_id	d4mlld_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.3 — beta-lactamase/transpeptidase-like
Superfamily Superfamily superfamily	e.3.1 — beta-lactamase/transpeptidase-like
Family Family family	e.3.1.1 — beta-Lactamase/D-ala carboxypeptidase

CATH v4.4 (4 domains)

Domain ID domain_id	4mllA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	710 — Beta-lactamase
Homologous superfamily homologous superfamily	10 — DD-peptidase/beta-lactamase superfamily

Domain ID domain_id	4mllB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	710 — Beta-lactamase
Homologous superfamily homologous superfamily	10 — DD-peptidase/beta-lactamase superfamily

Domain ID domain_id	4mllC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	710 — Beta-lactamase
Homologous superfamily homologous superfamily	10 — DD-peptidase/beta-lactamase superfamily

Domain ID domain_id	4mllD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	710 — Beta-lactamase
Homologous superfamily homologous superfamily	10 — DD-peptidase/beta-lactamase superfamily

▶

Unit-cell length a length_a	50.919 Å
Unit-cell length b length_b	72.609 Å
Unit-cell length c length_c	73.446 Å
Unit-cell angle α angle_alpha	80.90 °
Unit-cell angle β angle_beta	69.87 °
Unit-cell angle γ angle_gamma	71.44 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.370 Å
Low-resolution limit resolution_low	33.230 Å
R factor r_factor	0.1648
R_work r_work	0.1632
R_free r_free	0.1958

The 1.4 A structure of the class D beta-lactamase OXA-1 K70D complexed with oxacillin

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

Beta-lactamase OXA-1

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

4mll__assembly_4__model_1

4mll__assembly_4__model_1 | I(q)

4mll__assembly_4__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

The 1.4 A structure of the class D beta-lactamase OXA-1 K70D complexed with oxacillin

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

Beta-lactamase OXA-1

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

4mll__assembly_4__model_1

4mll__assembly_4__model_1 | I(q)

4mll__assembly_4__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)