SAXSdb — 9hkf

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

Haloalkane dehalogenase,non-specific serine/threonine protein kinase

Rhodococcus rhodochrous

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Monomer	Protein 1	CHLORIDE ION × 1 FLAVIN MONONUCLEOTIDE × 1 ;(1E,3S)-1-{10-[2-carboxy-5-({2-[2-(hexyloxy)ethoxy]ethyl}carbamoyl)phenyl]-7-(3-fluoroazetidin-1-yl)-5,5-dimethyldibenz o[b,e]silin-3(5H)-ylidene}-3-fluoroazetidin-1-ium ; × 1 GLYCEROL × 4 water × 1	Consistent with protein count
2	Insufficient information	Monomer	Protein 1	CHLORIDE ION × 1 FLAVIN MONONUCLEOTIDE × 1 ;(1E,3S)-1-{10-[2-carboxy-5-({2-[2-(hexyloxy)ethoxy]ethyl}carbamoyl)phenyl]-7-(3-fluoroazetidin-1-yl)-5,5-dimethyldibenz o[b,e]silin-3(5H)-ylidene}-3-fluoroazetidin-1-ium ; × 1 GLYCEROL × 7 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A453KFI0_AEGTS
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 149–284； UniProt 46–181 Author chain B； PDBConstruct 149–284； UniProt 46–181

Haloalkane dehalogenase,non-specific serine/threonine protein kinase

Rhodococcus rhodochrous

UniProt P0A3G2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Monomer	Protein 1	CHLORIDE ION × 1 FLAVIN MONONUCLEOTIDE × 1 ;(1E,3S)-1-{10-[2-carboxy-5-({2-[2-(hexyloxy)ethoxy]ethyl}carbamoyl)phenyl]-7-(3-fluoroazetidin-1-yl)-5,5-dimethyldibenz o[b,e]silin-3(5H)-ylidene}-3-fluoroazetidin-1-ium ; × 1 GLYCEROL × 4 water × 1	Consistent with protein count
2	Insufficient information	Monomer	Protein 1	CHLORIDE ION × 1 FLAVIN MONONUCLEOTIDE × 1 ;(1E,3S)-1-{10-[2-carboxy-5-({2-[2-(hexyloxy)ethoxy]ethyl}carbamoyl)phenyl]-7-(3-fluoroazetidin-1-yl)-5,5-dimethyldibenz o[b,e]silin-3(5H)-ylidene}-3-fluoroazetidin-1-ium ; × 1 GLYCEROL × 7 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 5–145； UniProt 3–143 Author chain A； PDBConstruct 286–432； UniProt 144–290 Author chain B； PDBConstruct 5–145； UniProt 3–143 Author chain B； PDBConstruct 286–432； UniProt 144–290

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	9hkf
Deposition date deposition_date	2024-12-03
Structure title title	X-Ray crystal structure of a photoswitchable HaloTag bound to JF635
Keywords keywords	HaloTag, LOV domain, FMN, dye, photoswitch, psHaloTag, Light-oxygen-voltage-sensing domain, rhodamine, BIOSYNTHETIC PROTEIN; BIOSYNTHETIC PROTEIN
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.

9hkf__assembly_1__model_1

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

Download this curve (.dat)

9hkf__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9hkf__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.40 Å
Rg (electron density)	23.23 Å
Total Rg	24.08 Å
Atom count	3602
Residues	432
Excluded volume	64204 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9hkf__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9hkf__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 (6)

Entity 1 Entity 1 polymer

Description description	Haloalkane dehalogenase,non-specific serine/threonine protein kinase
Molecular weight formula_weight	50100.9 kDa
EC 编号 ec_number	3.8.1.5,2.7.11.1
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,A
Atom count atom_count	7598

GPMAEIGTGFPFDPHYVEVLGERMHYVDVGPRDGTPVLFLHGNPTSSYVWRNIIPHVAPTHRCIAPDLIGMGKSDKPDLGYFFDDHVRFMDAFIEALGLEEVVLVIHDWGSALGFHWAKRNPERVKGIAFMEFIRPIPTWDEWPWFAGLERIEKNFIITDPRLPDNPIIFASDSFLQLTEYSREEILGRNCRFLQGPETDRATVRKIRDAIDNQTEVTVQLINYTKSGKKFWNLFHLQPMRDQKGDVQYFIGVQLDGTEHVRDAAEREGVMLIKKTAENIDEAAPFWRETFQAFRTTDVGRKLIIDQNVFIEGTLPMGVVRPLTEVEMDHYREPFLNPVDREPLWRFPNELPIAGEPANIVALVEEYMDWLHQSPVPKLLFWGTPGVLIPPAEAARLAKSLPNCKAVDIGPGLNLLQEDNPDLIGSEIARWLSTLEISG

Source Source

Source organism organism	Rhodococcus rhodochrous
NCBI taxonomy ID ncbi_taxonomy_id	1829
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

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

Entity 3 Entity 3 non-polymer

Description description	FLAVIN MONONUCLEOTIDE
Molecular weight formula_weight	456.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	;(1E,3S)-1-{10-[2-carboxy-5-({2-[2-(hexyloxy)ethoxy]ethyl}carbamoyl)phenyl]-7-(3-fluoroazetidin-1-yl)-5,5-dimethyldibenz o[b,e]silin-3(5H)-ylidene}-3-fluoroazetidin-1-ium ;
Molecular weight formula_weight	704.9 kDa
Source method src_method	nat
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	11

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	376

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Unit-cell length a length_a	167.737 Å
Unit-cell length b length_b	78.017 Å
Unit-cell length c length_c	81.807 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	103.92 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	70.360 Å
R factor r_factor	0.1881
R_work r_work	0.1855
R_free r_free	0.2354

X-Ray crystal structure of a photoswitchable HaloTag bound to JF635

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

Haloalkane dehalogenase,non-specific serine/threonine protein kinase

State in the Current Structure

Other States of the Same Protein in the Database

Haloalkane dehalogenase,non-specific serine/threonine protein kinase

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

9hkf__assembly_1__model_1

9hkf__assembly_1__model_1 | I(q)

9hkf__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 (6)

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 non-polymer

Entity 6 Entity 6 water

7. Citations (1)

X-Ray crystal structure of a photoswitchable HaloTag bound to JF635

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

Haloalkane dehalogenase,non-specific serine/threonine protein kinase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Haloalkane dehalogenase,non-specific serine/threonine protein kinase

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

9hkf__assembly_1__model_1

9hkf__assembly_1__model_1 | I(q)

9hkf__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 (6)

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 non-polymer

Entity 6 Entity 6 water

7. Citations (1)