SAXSdb — 4rl0

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

Beta-lactamase NDM-1

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	ZINC ION × 4 ;(2R,5S)-5-[(carbamoyloxy)methyl]-2-[(R)-carboxy{[(2Z)-2-(furan-2-yl)-2-(methoxyimino)acetyl]amino}methyl]-5,6-dihydro-2H-1,3-thiazine-4-carboxylic acid ; × 2 water × 2	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	ZINC ION × 2 ;(2R,5S)-5-[(carbamoyloxy)methyl]-2-[(R)-carboxy{[(2Z)-2-(furan-2-yl)-2-(methoxyimino)acetyl]amino}methyl]-5,6-dihydro-2H-1,3-thiazine-4-carboxylic acid ; × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	ZINC ION × 2 ;(2R,5S)-5-[(carbamoyloxy)methyl]-2-[(R)-carboxy{[(2Z)-2-(furan-2-yl)-2-(methoxyimino)acetyl]amino}methyl]-5,6-dihydro-2H-1,3-thiazine-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	BLAN1_KLEPN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–242； UniProt 29–270 Author chain B； PDBConstruct 1–242； UniProt 29–270

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	4rl0
Deposition date deposition_date	2014-10-14
Structure title title	Structural and mechanistic insights into NDM-1 catalyzed hydrolysis of cephalosporins
Keywords keywords	NDM-1 antibiotic hydrolysis, 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.

4rl0__assembly_1__model_1

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

Download this curve (.dat)

4rl0__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4rl0__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.45 Å
Rg (electron density)	24.13 Å
Total Rg	24.70 Å
Atom count	3593
Residues	469
Excluded volume	62741 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4rl0__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4rl0__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4rl0__assembly_3__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 (4)

Entity 1 Entity 1 polymer

Description description	Beta-lactamase NDM-1
Molecular weight formula_weight	25631.8 kDa
EC 编号 ec_number	3.5.2.6
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	4238

GEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR

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

Entity 3 Entity 3 non-polymer

Description description	;(2R,5S)-5-[(carbamoyloxy)methyl]-2-[(R)-carboxy{[(2Z)-2-(furan-2-yl)-2-(methoxyimino)acetyl]amino}methyl]-5,6-dihydro-2H-1,3-thiazine-4-carboxylic acid ;
Molecular weight formula_weight	442.4 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	645

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4rl0a_
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.157.1.0 — automated matches

Domain ID domain_id	d4rl0b_
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.157.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	4rl0A00
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	4rl0B00
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	39.180 Å
Unit-cell length b length_b	78.890 Å
Unit-cell length c length_c	133.060 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	8

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

Resolution resolution	1.300 Å
Low-resolution limit resolution_low	29.364 Å
R factor r_factor	0.1319
R_work r_work	0.1307
R_free r_free	0.1567

Structural and mechanistic insights into NDM-1 catalyzed hydrolysis of cephalosporins

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

Beta-lactamase NDM-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

4rl0__assembly_1__model_1

4rl0__assembly_1__model_1 | I(q)

4rl0__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 (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

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Structural and mechanistic insights into NDM-1 catalyzed hydrolysis of cephalosporins

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

Beta-lactamase NDM-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

4rl0__assembly_1__model_1

4rl0__assembly_1__model_1 | I(q)

4rl0__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 (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

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)