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- PDB-5y2y: Crystal structure of HaloTag (M175C) complexed with dansyl-PEG2-H... -

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Basic information

Entry
Database: PDB / ID: 5y2y
TitleCrystal structure of HaloTag (M175C) complexed with dansyl-PEG2-HaloTag ligand
ComponentsHaloalkane dehalogenase
KeywordsHYDROLASE / halotag / haloalkane dehalogenase / Dansyl ligand
Function / homology
Function and homology information


haloalkane dehalogenase / haloalkane dehalogenase activity / response to toxic substance / membrane
Similarity search - Function
Haloalkane dehalogenase, subfamily 2 / : / Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-8LL / Haloalkane dehalogenase
Similarity search - Component
Biological speciesRhodococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsLee, H. / Kang, M. / Rhee, H. / Lee, C.
CitationJournal: Chem. Commun. (Camb.) / Year: 2017
Title: Structure-guided synthesis of a protein-based fluorescent sensor for alkyl halides
Authors: Kang, M.G. / Lee, H. / Kim, B.H. / Dunbayev, Y. / Seo, J.K. / Lee, C. / Rhee, H.W.
History
DepositionJul 27, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 6, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Sep 17, 2025Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_unobs_or_zero_occ_atoms ...pdbx_entry_details / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Haloalkane dehalogenase
B: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,3496
Polymers67,4332
Non-polymers9164
Water5,729318
1
A: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1743
Polymers33,7161
Non-polymers4582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-12 kcal/mol
Surface area11240 Å2
MethodPISA
2
B: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1743
Polymers33,7161
Non-polymers4582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-12 kcal/mol
Surface area11170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.393, 72.355, 174.942
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Haloalkane dehalogenase


Mass: 33716.398 Da / Num. of mol.: 2
Mutation: S2A, L47V, S58T, D78G, Y87F, L88M, C128F, A155T, E160K, A167V, A172T, K175C, C176G, K195N, A224E, N227D, E257K, T264A, H272N, Y273L, P291S, A292T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus sp. (bacteria) / Gene: dhaA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A3G3, haloalkane dehalogenase
#2: Chemical ChemComp-8LL / 5-(dimethylamino)-~{N}-[2-(2-hexoxyethoxy)ethyl]naphthalene-1-sulfonamide


Mass: 422.581 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H34N2O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / Source method: isolated from a natural source / Formula: H2O
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: 2.08 Å3/Da / Density % sol: 40.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.8M ammonium sulfate, 0.1M citric acid pH5.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.27→50 Å / Num. obs: 26399 / % possible obs: 98.4 % / Redundancy: 10.4 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 56.1
Reflection shellResolution: 2.27→2.31 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.073 / Mean I/σ(I) obs: 38.6 / % possible all: 88

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Processing

Software
NameVersionClassification
HKL-2000data processing
PHENIX1.10.1-2155phasing
Cootmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KAF

4kaf


Resolution: 2.27→34.73 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.216 1315 -
Rwork0.158 --
obs0.161 26291 98.17 %
Refinement stepCycle: LAST / Resolution: 2.27→34.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4704 0 26 318 5048
LS refinement shellResolution: 2.2742→2.3653 Å / Rfactor Rfree: 0.217 / Rfactor Rwork: 0.14

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