SAXSdb — 8pec

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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 2	;1-({(2R)-2-[(1R)-1-{[(2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-{[(2-carboxypropan-2-yl)oxy]imino}acetyl]amino}-2-oxoethyl]-4-carboxy-3,6-dihydro-2H-1,3-thiazin-5-yl}methyl)pyridinium ; × 1 CHLORIDE ION × 1 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	;1-({(2R)-2-[(1R)-1-{[(2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-{[(2-carboxypropan-2-yl)oxy]imino}acetyl]amino}-2-oxoethyl]-4-carboxy-3,6-dihydro-2H-1,3-thiazin-5-yl}methyl)pyridinium ; × 2 CHLORIDE ION × 1 water × 2	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 A； PDBConstruct 1–242； UniProt 24–265 Author chain B； PDBConstruct 1–242； UniProt 24–265 Author chain C； PDBConstruct 1–242； UniProt 24–265 Author chain D； PDBConstruct 1–242； UniProt 24–265

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	8pec
Deposition date deposition_date	2023-06-13
Structure title title	OXA-48_Q5-CAZ. Epistasis Arises from Shifting the Rate-Limiting Step during Enzyme Evolution
Keywords keywords	Protein evolution. Antibiotic resistance. OXA-48. HYDROLASE. Serine-Beta-lactamase., 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.

8pec__assembly_2__model_1

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

Download this curve (.dat)

8pec__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8pec__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	24.61 Å
Rg (electron density)	23.44 Å
Total Rg	24.32 Å
Atom count	3847
Residues	454
Excluded volume	67400 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8pec__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`8pec__assembly_2__model_1`	dimeric （2）	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 (4)

Entity 1 Entity 1 polymer

Description description	Beta-lactamase
Molecular weight formula_weight	28002.7 kDa
EC 编号 ec_number	3.5.2.6
Mutation mutation	A33V, K51E, F72L, S212A, T213A
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	7736

EWQENKSWNVHFTEHKSQGVVVLWNENEQQGFTNNLKRANQAFLPASTLKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYAARIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP

Source Source

Source organism organism	Klebsiella pneumoniae
NCBI taxonomy ID ncbi_taxonomy_id	573
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	;1-({(2R)-2-[(1R)-1-{[(2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-{[(2-carboxypropan-2-yl)oxy]imino}acetyl]amino}-2-oxoethyl]-4-carboxy-3,6-dihydro-2H-1,3-thiazin-5-yl}methyl)pyridinium ;
Molecular weight formula_weight	549.6 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	84

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Unit-cell length a length_a	202.147 Å
Unit-cell length b length_b	202.147 Å
Unit-cell length c length_c	55.699 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	24

Space group space_group	P 61
Space-group number int_tables_number	169
Crystal system crystal_system	hexagonal

Resolution resolution	2.660 Å
Low-resolution limit resolution_low	24.390 Å
R factor r_factor	0.2055
R_work r_work	0.2023
R_free r_free	0.2707

OXA-48_Q5-CAZ. Epistasis Arises from Shifting the Rate-Limiting Step during Enzyme Evolution

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

8pec__assembly_2__model_1

8pec__assembly_2__model_1 | I(q)

8pec__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 (4)

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 water

7. Citations (1)

OXA-48_Q5-CAZ. Epistasis Arises from Shifting the Rate-Limiting Step during Enzyme Evolution

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

8pec__assembly_2__model_1

8pec__assembly_2__model_1 | I(q)

8pec__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 (4)

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 water

7. Citations (1)