SAXSdb — 3bff

▼

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

Class A beta-lactamase Sed1

Citrobacter sedlakii

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	THIOCYANATE ION × 1 (2R)-2-[(1S,2R)-1-carboxy-2-hydroxypropyl]-5-[(2R)-oxolan-2-yl]-2,3-dihydro-1,3-thiazole-4-carboxylic acid × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	THIOCYANATE ION × 3 (2R)-2-[(1S,2R)-1-carboxy-2-hydroxypropyl]-5-[(2R)-oxolan-2-yl]-2,3-dihydro-1,3-thiazole-4-carboxylic acid × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	THIOCYANATE ION × 1 (2R)-2-[(1S,2R)-1-carboxy-2-hydroxypropyl]-5-[(2R)-oxolan-2-yl]-2,3-dihydro-1,3-thiazole-4-carboxylic acid × 1 (5R,6S)-6-(1-hydroxyethyl)-7-oxo-3-[(2R)-oxolan-2-yl]-4-thia-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	THIOCYANATE ION × 1 (2R)-2-[(1S,2R)-1-carboxy-2-hydroxypropyl]-5-[(2R)-oxolan-2-yl]-2,3-dihydro-1,3-thiazole-4-carboxylic acid × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q93PQ0_9ENTR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–262； UniProt 34–295 Author chain B； PDBConstruct 1–262； UniProt 34–295 Author chain C； PDBConstruct 1–262； UniProt 34–295 Author chain D； PDBConstruct 1–262； UniProt 34–295

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	3bff
Deposition date deposition_date	2007-11-21
Structure title title	class A beta-lactamase SED-G238C complexed with faropenem
Keywords keywords	HYDROLASE, BETA-LACTAMASE, CLASS A SED-G238C, FAROPENEM, ACYL-ENZYME; 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.

3bff__assembly_1__model_1

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

Download this curve (.dat)

3bff__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3bff__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	18.61 Å
Rg (electron density)	17.60 Å
Total Rg	18.52 Å
Atom count	2009
Residues	262
Excluded volume	35737 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3bff__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3bff__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3bff__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3bff__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	Class A beta-lactamase Sed1
Molecular weight formula_weight	28330.2 kDa
EC 编号 ec_number	3.5.2.6
Mutation mutation	G238C
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	9194

VQQVQKKLAALEKQSGGRLGVALINTADNSQVLYRADERFAMCSTSKVMTAAAVLKQSETHDGILQQKMTIKKADLTNWNPVTEKYVGNTMTLAELSAATLQYSDNTAMNKLLAHLGGPGNVTAFARSIGDTTFRLDRKEPELNTAIPGDERDTTSPLAMAKSLRKLTLGDALAGPQRAQLVDWLKGNTTGGQSIRAGLPAHWVVGDKTGACDYGTTNDIAVIWPEDRAPLVLVTYFTQPQQDAKWRKDVLAAAAKIVTEGK

Source Source

Source organism organism	Citrobacter sedlakii
NCBI taxonomy ID ncbi_taxonomy_id	67826
Host organism host_organism	Escherichia coli BL21

Entity 2 Entity 2 non-polymer

Description description	THIOCYANATE ION
Molecular weight formula_weight	58.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	(2R)-2-[(1S,2R)-1-carboxy-2-hydroxypropyl]-5-[(2R)-oxolan-2-yl]-2,3-dihydro-1,3-thiazole-4-carboxylic acid
Molecular weight formula_weight	303.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	(5R,6S)-6-(1-hydroxyethyl)-7-oxo-3-[(2R)-oxolan-2-yl]-4-thia-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid
Molecular weight formula_weight	285.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1133

▼

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3bffa_
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	d3bffb_
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	d3bffc_
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	d3bffd_
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	3bffA00
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	3bffB00
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	3bffC00
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	3bffD00
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	187.116 Å
Unit-cell length b length_b	73.244 Å
Unit-cell length c length_c	103.504 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	121.69 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

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

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	28.800 Å
R factor r_factor	0.1890
R_work r_work	0.1800
R_free r_free	0.2050

class A beta-lactamase SED-G238C complexed with faropenem

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

Class A beta-lactamase Sed1

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

3bff__assembly_1__model_1

3bff__assembly_1__model_1 | I(q)

3bff__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 (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 (2)

class A beta-lactamase SED-G238C complexed with faropenem

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

Class A beta-lactamase Sed1

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

3bff__assembly_1__model_1

3bff__assembly_1__model_1 | I(q)

3bff__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 (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 (2)