SAXSdb — 2bfk

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

BETA-LACTAMASE II

BACILLUS CEREUS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	AZIDE ION × 1 GLYCEROL × 10 ZINC ION × 2 SULFATE ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	AZIDE ION × 1 GLYCEROL × 6 ZINC ION × 2 SULFATE ION × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BLA2_BACCE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–19； UniProt 31–49 Author chain A； PDBConstruct 20–37； UniProt 50–67 Author chain A； PDBConstruct 38–72； UniProt 68–102 Author chain A； PDBConstruct 73–78； UniProt 103–108 Author chain A； PDBConstruct 79–101； UniProt 109–131 Author chain A； PDBConstruct 102–119； UniProt 132–149 Author chain A； PDBConstruct 120–158； UniProt 150–188 Author chain A； PDBConstruct 159–161； UniProt 189–191 Author chain A； PDBConstruct 162–212； UniProt 192–242 Author chain A； PDBConstruct 213–227； UniProt 243–257 Author chain B； PDBConstruct 1–19； UniProt 31–49 Author chain B； PDBConstruct 20–37； UniProt 50–67 Author chain B； PDBConstruct 38–72； UniProt 68–102 Author chain B； PDBConstruct 73–78； UniProt 103–108 Author chain B； PDBConstruct 79–101； UniProt 109–131 Author chain B； PDBConstruct 102–119； UniProt 132–149 Author chain B； PDBConstruct 120–158； UniProt 150–188 Author chain B； PDBConstruct 159–161； UniProt 189–191 Author chain B； PDBConstruct 162–212； UniProt 192–242 Author chain B； PDBConstruct 213–227； UniProt 243–257

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	2bfk
Deposition date deposition_date	2004-12-07
Structure title title	Bacillus cereus metallo-beta-lactamase (BcII) Arg (121) Cys mutant. Solved at pH7 using 20mM ZnSO4 in buffer. 1mM DTT was used as a reducing agent
Keywords keywords	HYDROLASE, ZINC, METALLO-BETA-LACTAMASE, ANTIBIOTIC RESISTANCE; 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.

2bfk__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2bfk__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2bfk__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	17.36 Å
Rg (electron density)	16.17 Å
Total Rg	17.30 Å
Atom count	1752
Residues	220
Excluded volume	31405 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2bfk__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2bfk__assembly_2__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 (6)

Entity 1 Entity 1 polymer

Description description	BETA-LACTAMASE II
Molecular weight formula_weight	24941.5 kDa
EC 编号 ec_number	3.5.2.6
Mutation mutation	YES
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	4079

SQKVEKTVIKNETGTISISQLNKNVWVHTELGSFNGEAVPSNGLVLNTSKGLVLVDSSWDDKLTKELIEMVEKKFQKRVTDVIITHAHADCIGGIKTLKERGIKAHSTALTAELAKKNGYEEPLGDLQTVTNLKFGNMKVETFYPGKGHTEDNIVVWLPQYNILVGGCLVKSTSAKDLGNVADAYVNEWSTSIENVLKRYRNINAVVPGHGEVGDKGLLLHTLDLLK

Source Source

Source organism organism	BACILLUS CEREUS
NCBI taxonomy ID ncbi_taxonomy_id	1396
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	AZIDE ION
Molecular weight formula_weight	42.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	16

Entity 4 Entity 4 non-polymer

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

Entity 5 Entity 5 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	515

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2bfka_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.157 — Metallo-hydrolase/oxidoreductase
Superfamily Superfamily superfamily	d.157.1 — Metallo-hydrolase/oxidoreductase
Family Family family	d.157.1.1 — Zn metallo-beta-lactamase

Domain ID domain_id	d2bfkb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.157 — Metallo-hydrolase/oxidoreductase
Superfamily Superfamily superfamily	d.157.1 — Metallo-hydrolase/oxidoreductase
Family Family family	d.157.1.1 — Zn metallo-beta-lactamase

CATH v4.4 (2 domains)

Domain ID domain_id	2bfkA00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	15 — Metallo-beta-lactamase; Chain A
Homologous superfamily homologous superfamily	10 — Ribonuclease Z/Hydroxyacylglutathione hydrolase-like

Domain ID domain_id	2bfkB00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	15 — Metallo-beta-lactamase; Chain A
Homologous superfamily homologous superfamily	10 — Ribonuclease Z/Hydroxyacylglutathione hydrolase-like

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Unit-cell length a length_a	67.311 Å
Unit-cell length b length_b	67.311 Å
Unit-cell length c length_c	178.010 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	6.000 Å
R factor r_factor	0.1721
R_work r_work	0.1721
R_free r_free	0.2085

Bacillus cereus metallo-beta-lactamase (BcII) Arg (121) Cys mutant. Solved at pH7 using 20mM ZnSO4 in buffer. 1mM DTT was used as a reducing agent

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

BETA-LACTAMASE II

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

2bfk__assembly_2__model_1

2bfk__assembly_2__model_1 | I(q)

2bfk__assembly_2__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 (6)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (3)

Bacillus cereus metallo-beta-lactamase (BcII) Arg (121) Cys mutant. Solved at pH7 using 20mM ZnSO4 in buffer. 1mM DTT was used as a reducing agent

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

BETA-LACTAMASE II

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

2bfk__assembly_2__model_1

2bfk__assembly_2__model_1 | I(q)

2bfk__assembly_2__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 (6)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (3)