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- PDB-9hkf: X-Ray crystal structure of a photoswitchable HaloTag bound to JF635 -

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Basic information

Entry
Database: PDB / ID: 9hkf
TitleX-Ray crystal structure of a photoswitchable HaloTag bound to JF635
ComponentsHaloalkane dehalogenase,non-specific serine/threonine protein kinase
KeywordsBIOSYNTHETIC PROTEIN / HaloTag / LOV domain / FMN / dye / photoswitch / psHaloTag / Light-oxygen-voltage-sensing domain / rhodamine
Function / homology
Function and homology information


haloalkane dehalogenase / haloalkane dehalogenase activity / response to blue light / photoreceptor activity / response to toxic substance / protein kinase activity / ATP binding / nucleus / membrane
Similarity search - Function
Haloalkane dehalogenase, subfamily 2 / : / PAS domain / PAS-associated, C-terminal / PAC domain profile. / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 ...Haloalkane dehalogenase, subfamily 2 / : / PAS domain / PAS-associated, C-terminal / PAC domain profile. / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / PAS repeat profile. / PAS domain / PAS domain superfamily / Alpha/Beta hydrolase fold / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Chem-PUJ / LOV domain-containing protein / Haloalkane dehalogenase
Similarity search - Component
Biological speciesRhodococcus rhodochrous (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsWeidenhausen, J. / Ugarte-Uribe, B. / Walterspiel, F. / Mueller, C.W. / Deo, C.
Funding support United States, 2items
OrganizationGrant numberCountry
Chan Zuckerberg Initiative2020-225346 United States
Chan Zuckerberg Initiative2024-337799 United States
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2025
Title: A Photoswitchable HaloTag for Spatiotemporal Control of Fluorescence in Living Cells.
Authors: Walterspiel, F. / Ugarte-Uribe, B. / Weidenhausen, J. / Vincent, M. / Narayanasamy, K.K. / Dimitriadi, A. / Khan, A.U.M. / Fritsch, M. / Muller, C.W. / Zimmermann, T. / Deo, C.
History
DepositionDec 3, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Haloalkane dehalogenase,non-specific serine/threonine protein kinase
A: Haloalkane dehalogenase,non-specific serine/threonine protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,60819
Polymers100,2022
Non-polymers3,40617
Water6,774376
1
B: Haloalkane dehalogenase,non-specific serine/threonine protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6668
Polymers50,1011
Non-polymers1,5657
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Haloalkane dehalogenase,non-specific serine/threonine protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,94211
Polymers50,1011
Non-polymers1,84110
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)167.737, 78.017, 81.807
Angle α, β, γ (deg.)90.00, 103.92, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules BA

#1: Protein Haloalkane dehalogenase,non-specific serine/threonine protein kinase


Mass: 50100.949 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: psHaloTag1a (synthetic HaloTag with LOV domain) after proteolytical cleavage of the N-terminal His-tag,psHaloTag1a (synthetic HaloTag with LOV domain) after proteolytical cleavage of the N- ...Details: psHaloTag1a (synthetic HaloTag with LOV domain) after proteolytical cleavage of the N-terminal His-tag,psHaloTag1a (synthetic HaloTag with LOV domain) after proteolytical cleavage of the N-terminal His-tag,psHaloTag1a (synthetic HaloTag with LOV domain) after proteolytical cleavage of the N-terminal His-tag,psHaloTag1a (synthetic HaloTag with LOV domain) after proteolytical cleavage of the N-terminal His-tag,psHaloTag1a (synthetic HaloTag with LOV domain) after proteolytical cleavage of the N-terminal His-tag,psHaloTag1a (synthetic HaloTag with LOV domain) after proteolytical cleavage of the N-terminal His-tag,psHaloTag1a (synthetic HaloTag with LOV domain) after proteolytical cleavage of the N-terminal His-tag,psHaloTag1a (synthetic HaloTag with LOV domain) after proteolytical cleavage of the N-terminal His-tag,psHaloTag1a (synthetic HaloTag with LOV domain) after proteolytical cleavage of the N-terminal His-tag,psHaloTag1a (synthetic HaloTag with LOV domain) after proteolytical cleavage of the N-terminal His-tag,psHaloTag1a (synthetic HaloTag with LOV domain) after proteolytical cleavage of the N-terminal His-tag,psHaloTag1a (synthetic HaloTag with LOV domain) after proteolytical cleavage of the N-terminal His-tag,psHaloTag1a (synthetic HaloTag with LOV domain) after proteolytical cleavage of the N-terminal His-tag,psHaloTag1a (synthetic HaloTag with LOV domain) after proteolytical cleavage of the N-terminal His-tag,psHaloTag1a (synthetic HaloTag with LOV domain) after proteolytical cleavage of the N-terminal His-tag,psHaloTag1a (synthetic HaloTag with LOV domain) after proteolytical cleavage of the N-terminal His-tag,psHaloTag1a (synthetic HaloTag with LOV domain) after proteolytical cleavage of the N-terminal His-tag,psHaloTag1a (synthetic HaloTag with LOV domain) after proteolytical cleavage of the N-terminal His-tag,psHaloTag1a (synthetic HaloTag with LOV domain) after proteolytical cleavage of the N-terminal His-tag,psHaloTag1a (synthetic HaloTag with LOV domain) after proteolytical cleavage of the N-terminal His-tag,psHaloTag1a (synthetic HaloTag with LOV domain) after proteolytical cleavage of the N-terminal His-tag,psHaloTag1a (synthetic HaloTag with LOV domain) after proteolytical cleavage of the N-terminal His-tag,psHaloTag1a (synthetic HaloTag with LOV domain) after proteolytical cleavage of the N-terminal His-tag,psHaloTag1a (synthetic HaloTag with LOV domain) after proteolytical cleavage of the N-terminal His-tag,psHaloTag1a (synthetic HaloTag with LOV domain) after proteolytical cleavage of the N-terminal His-tag,psHaloTag1a (synthetic HaloTag with LOV domain) after proteolytical cleavage of the N-terminal His-tag,psHaloTag1a (synthetic HaloTag with LOV domain) after proteolytical cleavage of the N-terminal His-tag
Source: (gene. exp.) Rhodococcus rhodochrous (bacteria) / Gene: dhaA / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0A3G2, UniProt: A0A453KFI0, haloalkane dehalogenase, non-specific serine/threonine protein kinase

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Non-polymers , 5 types, 393 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PUJ / (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 / JF635


Mass: 704.898 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C39H48F2N3O5Si / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 376 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.56 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: crystallization condition: (0.1 M Bis-Tris propane pH 6.5, 0.2 M sodium nitrate, 20% (w/v) PEG3350, 10% (v/v) ethylene glycol); mixed 1:1 with protein in buffer (20 mM Tris-HCl pH 7.4, 100 mM NaCl)
Temp details: 20C

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8731 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: May 19, 2024 / Details: KB mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 2.4→70.36 Å / Num. obs: 40131 / % possible obs: 99.7 % / Redundancy: 7 % / CC1/2: 0.985 / Rmerge(I) obs: 0.294 / Rpim(I) all: 0.119 / Rrim(I) all: 0.318 / Χ2: 1.02 / Net I/σ(I): 5.1 / Num. measured all: 280654
Reflection shellResolution: 2.4→2.49 Å / % possible obs: 99.7 % / Redundancy: 7.1 % / Rmerge(I) obs: 1.702 / Num. measured all: 29943 / Num. unique obs: 4203 / CC1/2: 0.58 / Rpim(I) all: 0.682 / Rrim(I) all: 1.835 / Χ2: 0.96 / Net I/σ(I) obs: 1.1

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Processing

Software
NameVersionClassification
XDSv1.13data reduction
Aimless8.0.008data scaling
PHASER(1.20.1_4487:000)phasing
PHENIX(1.20.1_4487:000)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→70.36 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2354 2039 5.08 %aimless random 5%
Rwork0.1855 ---
obs0.1881 40102 99.56 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→70.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6992 0 230 379 7601
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097431
X-RAY DIFFRACTIONf_angle_d1.01210125
X-RAY DIFFRACTIONf_dihedral_angle_d15.9271010
X-RAY DIFFRACTIONf_chiral_restr0.0561056
X-RAY DIFFRACTIONf_plane_restr0.0091302
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.28391270.25832516X-RAY DIFFRACTION100
2.46-2.520.36451370.26012528X-RAY DIFFRACTION100
2.52-2.590.28231220.24912536X-RAY DIFFRACTION100
2.59-2.660.36071360.25752531X-RAY DIFFRACTION100
2.66-2.750.29021320.24252519X-RAY DIFFRACTION100
2.75-2.850.28611440.23042498X-RAY DIFFRACTION100
2.85-2.960.27151450.22562531X-RAY DIFFRACTION100
2.96-3.090.28511450.2132520X-RAY DIFFRACTION100
3.09-3.260.24191400.18172535X-RAY DIFFRACTION100
3.26-3.460.23451430.17522515X-RAY DIFFRACTION100
3.46-3.730.22181420.16742563X-RAY DIFFRACTION100
3.73-4.10.1991420.15912525X-RAY DIFFRACTION100
4.1-4.70.18851390.13722540X-RAY DIFFRACTION99
4.7-5.920.19351170.16512579X-RAY DIFFRACTION99
5.92-70.360.19651280.16852627X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.74140.68320.55662.12631.16011.5722-0.00620.06390.028-0.19960.0203-0.0989-0.142-0.0044-0.020.22810.0261-0.02090.19930.03970.2168-27.509618.088218.0389
23.4431.59570.522.52050.42942.43140.14710.3753-0.42590.0398-0.11870.09670.8499-0.31920.05390.55680.0136-0.03440.32150.02650.2963-36.1287-5.047418.6632
31.72970.1560.34422.29980.22692.1225-0.02580.04830.0343-0.06470.0115-0.0314-0.0188-0.03460.02230.2215-0.0161-0.00260.1491-0.01910.1985-28.308621.760223.7253
41.3382-0.8933-0.81251.97481.04391.2116-0.0308-0.0909-0.09480.22270.00670.05610.09070.02890.00360.3028-0.0250.00210.21930.02050.1993-33.1121-10.2155.3376
53.4009-0.6196-0.41925.52651.43673.32740.0188-0.05830.54-0.07060.2285-0.2418-1.04370.1991-0.21780.67110.0230.09010.4713-0.00090.4308-43.29816.049158.3965
61.4033-0.6798-0.68342.76890.25580.9716-0.04230.0071-0.10550.11490.03640.10320.0368-0.0946-0.00830.2973-0.0147-0.01350.2205-0.00390.2-33.1734-10.351849.1954
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 239 )
2X-RAY DIFFRACTION2chain 'A' and (resid 240 through 292 )
3X-RAY DIFFRACTION3chain 'A' and (resid 293 through 434 )
4X-RAY DIFFRACTION4chain 'B' and (resid 4 through 239 )
5X-RAY DIFFRACTION5chain 'B' and (resid 240 through 267 )
6X-RAY DIFFRACTION6chain 'B' and (resid 268 through 434 )

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