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- PDB-5y2x: Crystal structure of apo-HaloTag (M175C) -

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Basic information

Entry
Database: PDB / ID: 5y2x
TitleCrystal structure of apo-HaloTag (M175C)
ComponentsHaloalkane dehalogenase
KeywordsHYDROLASE / halotag / haloalkane dehalogenase
Function / homology
Function and homology information


haloalkane dehalogenase / haloalkane dehalogenase activity / response to toxic substance
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
Haloalkane dehalogenase
Similarity search - Component
Biological speciesRhodococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 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: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7522
Polymers33,7161
Non-polymers351
Water4,666259
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-12 kcal/mol
Surface area11690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.642, 62.642, 164.192
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Haloalkane dehalogenase /


Mass: 33716.398 Da / Num. of mol.: 1 / Fragment: UNP residues 2-293
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-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O

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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: 2.39 Å3/Da / Density % sol: 48.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 25% PEG 20K, 0.1M Tris pH 8.2, 200mM MgCl2, 5% butanol.

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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: 2.02→50 Å / Num. obs: 22255 / % possible obs: 99.5 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 26.4
Reflection shellRmerge(I) obs: 0.334

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Processing

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

4kaf


Resolution: 2.02→34.44 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.192 1109 -
Rwork0.163 --
obs-22178 99.93 %
Refinement stepCycle: LAST / Resolution: 2.02→34.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2362 0 1 259 2622

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