SAXSdb — 5vnp

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

Haloalkane dehalogenase

Rhodococcus rhodochrous

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	N-{2-[2-(hexyloxy)ethoxy]ethyl}-N~2~-methyl-N~2~-{[7-(methylamino)-2,1,3-benzoxadiazol-4-yl]sulfonyl}glycinamide × 1 CHLORIDE ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	N-{2-[2-(hexyloxy)ethoxy]ethyl}-N~2~-methyl-N~2~-{[7-(methylamino)-2,1,3-benzoxadiazol-4-yl]sulfonyl}glycinamide × 1 CHLORIDE ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DHAA_RHORH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–290； UniProt 4–293 Author chain B； PDBConstruct 1–290； UniProt 4–293

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	5vnp
Deposition date deposition_date	2017-05-01
Structure title title	X-ray crystal structure of Halotag bound to the P1 benzoxadiazole fluorogenic ligand
Keywords keywords	biosensor, cytotoxicity, fluorescent probe, protein aggregation, proteome stress, 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.

5vnp__assembly_2__model_1

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

Download this curve (.dat)

5vnp__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5vnp__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	19.05 Å
Rg (electron density)	17.60 Å
Total Rg	18.64 Å
Atom count	2361
Residues	290
Excluded volume	42174 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5vnp__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5vnp__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 (4)

Entity 1 Entity 1 polymer

Description description	Haloalkane dehalogenase
Molecular weight formula_weight	32926.7 kDa
EC 编号 ec_number	3.8.1.5
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	4803

IGTGFPFDPHYVEVLGERMHYVDVGPRDGTPVLFLHGNPTSSYVWRNIIPHVAPTHRCIAPDLIGMGKSDKPDLGYFFDDHVRFMDAFIEALGLEEVVLVIHDWGSALGFHWAKRNPERVKGIAFMEFIRPIPTWDEWPEFARETFQAFRTTDVGRKLIIDQNVFIEGTLPMGVVRPLTEVEMDHYREPFLNPVDREPLWRFPNELPIAGEPANIVALVEEYMDWLHQSPVPKLLFWGTPGVLIPPAEAARLAKSLPNCKAVDIGPGLNLLQEDNPDLIGSEIARWLSTL

Source Source

Source organism organism	Rhodococcus rhodochrous
NCBI taxonomy ID ncbi_taxonomy_id	1829
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	N-{2-[2-(hexyloxy)ethoxy]ethyl}-N~2~-methyl-N~2~-{[7-(methylamino)-2,1,3-benzoxadiazol-4-yl]sulfonyl}glycinamide
Molecular weight formula_weight	471.6 kDa
Source method src_method	syn
Copy count entity_count	2

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	81

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5vnpa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamily	c.69.1 — alpha/beta-Hydrolases
Family Family family	c.69.1.8 — Haloalkane dehalogenase

Domain ID domain_id	d5vnpb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamily	c.69.1 — alpha/beta-Hydrolases
Family Family family	c.69.1.8 — Haloalkane dehalogenase

CATH v4.4 (2 domains)

Domain ID domain_id	5vnpA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

Domain ID domain_id	5vnpB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

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Unit-cell length a length_a	44.272 Å
Unit-cell length b length_b	69.481 Å
Unit-cell length c length_c	88.950 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.82 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.230 Å
Low-resolution limit resolution_low	44.000 Å
R factor r_factor	0.1991
R_work r_work	0.1975
R_free r_free	0.2286

X-ray crystal structure of Halotag bound to the P1 benzoxadiazole fluorogenic ligand

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

Haloalkane dehalogenase

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

5vnp__assembly_2__model_1

5vnp__assembly_2__model_1 | I(q)

5vnp__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

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

X-ray crystal structure of Halotag bound to the P1 benzoxadiazole fluorogenic ligand

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

Haloalkane dehalogenase

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

5vnp__assembly_2__model_1

5vnp__assembly_2__model_1 | I(q)

5vnp__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

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)