SAXSdb — 8qnz

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

Beta-lactamase

Klebsiella pneumoniae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	;(2R)-2-[(2S,3R)-1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-4-(2-methanimidamidoethylsulfanyl)-2,3-dihydro-1H-pyrrole -5-carboxylic acid ; × 3 BROMIDE ION × 11 1-BUTANOL × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q6XEC0_KLEPN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain AAA； PDBConstruct 18–260； UniProt 23–265 Author chain BBB； PDBConstruct 18–260； UniProt 23–265 Author chain CCC； PDBConstruct 18–260； UniProt 23–265 Author chain DDD； PDBConstruct 18–260； UniProt 23–265

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	8qnz
Deposition date deposition_date	2023-09-27
Structure title title	OXA-48 with carbamylated Lys73 in complex with hydrolysed Imipenem and bromide ion competing for binding with Arg250 at neutral pH
Keywords keywords	OXA, Imipenem, HYDROLASE; 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.

8qnz__assembly_1__model_1

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

Download this curve (.dat)

8qnz__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8qnz__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	39.46 Å
Rg (electron density)	39.93 Å
Total Rg	39.94 Å
Atom count	16008
Residues	973
Excluded volume	143400 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8qnz__assembly_1__model_1`	tetrameric （4）	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 (5)

Entity 1 Entity 1 polymer

Description description	Beta-lactamase
Molecular weight formula_weight	30254.1 kDa
EC 编号 ec_number	3.5.2.6
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	AAA,BBB,CCC,DDD
Atom count atom_count	17322

MHHHHHHSAGENLYFQGKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP

Source Source

Source organism organism	Klebsiella pneumoniae
NCBI taxonomy ID ncbi_taxonomy_id	573
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	;(2R)-2-[(2S,3R)-1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-4-(2-methanimidamidoethylsulfanyl)-2,3-dihydro-1H-pyrrole -5-carboxylic acid ;
Molecular weight formula_weight	317.4 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	BROMIDE ION
Molecular weight formula_weight	79.9 kDa
Source method src_method	syn
Copy count entity_count	11

Entity 4 Entity 4 non-polymer

Description description	1-BUTANOL
Molecular weight formula_weight	74.1 kDa
Source method src_method	nat
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	1019

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Unit-cell length a length_a	81.310 Å
Unit-cell length b length_b	105.965 Å
Unit-cell length c length_c	124.679 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	16

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.530 Å
Low-resolution limit resolution_low	62.417 Å
R factor r_factor	—
R_work r_work	0.1463
R_free r_free	0.1988

OXA-48 with carbamylated Lys73 in complex with hydrolysed Imipenem and bromide ion competing for binding with Arg250 at neutral pH

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

Beta-lactamase

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

8qnz__assembly_1__model_1

8qnz__assembly_1__model_1 | I(q)

8qnz__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

7. Citations (1)

OXA-48 with carbamylated Lys73 in complex with hydrolysed Imipenem and bromide ion competing for binding with Arg250 at neutral pH

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

Beta-lactamase

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

8qnz__assembly_1__model_1

8qnz__assembly_1__model_1 | I(q)

8qnz__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

7. Citations (1)