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- PDB-8b6r: X-ray structure of the haloalkane dehalogenase HaloTag7 labeled w... -

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Basic information

Entry
Database: PDB / ID: 8b6r
TitleX-ray structure of the haloalkane dehalogenase HaloTag7 labeled with a chloroalkane Cyanine3 fluorophore substrate
ComponentsHaloalkane dehalogenase
KeywordsHYDROLASE / haloalkane dehalogenase / HaloTag / HaloTag7 / Self-Labeling Protein / fluorophore / cyanine 3 / Cy3
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
Similarity search - Domain/homology
Chem-PJI / Haloalkane dehalogenase
Similarity search - Component
Biological speciesRhodococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsTarnawski, M. / Hellweg, L. / Hiblot, J.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Nat.Chem.Biol. / Year: 2023
Title: A general method for the development of multicolor biosensors with large dynamic ranges.
Authors: Hellweg, L. / Edenhofer, A. / Barck, L. / Huppertz, M.C. / Frei, M.S. / Tarnawski, M. / Bergner, A. / Koch, B. / Johnsson, K. / Hiblot, J.
History
DepositionSep 27, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3178
Polymers33,2261
Non-polymers1,0917
Water5,350297
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.560, 112.560, 44.330
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Space group name HallP4n2n
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/2
#3: y+1/2,-x+1/2,z+1/2
#4: x+1/2,-y+1/2,-z+1/2
#5: -x+1/2,y+1/2,-z+1/2
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
Components on special symmetry positions
IDModelComponents
11A-514-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Haloalkane dehalogenase /


Mass: 33225.980 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus sp. (bacteria) / Gene: dhaA / Production host: Escherichia coli (E. coli) / References: UniProt: P0A3G3, haloalkane dehalogenase

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Non-polymers , 5 types, 304 molecules

#2: Chemical ChemComp-PJI / ~{N}-[2-[2-(6-chloranylhexoxy)ethoxy]ethyl]-6-[3,3-dimethyl-2-[(~{E})-3-(1,3,3-trimethylindol-2-ylidene)prop-1-enyl]indol-1-ium-1-yl]hexanamide


Mass: 663.352 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H57ClN3O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 297 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.11 Å3/Da / Density % sol: 41.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.2 M magnesium acetate, 19% (m/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.999884 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 30, 2020
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999884 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 46121 / % possible obs: 99.9 % / Redundancy: 7.4 % / Biso Wilson estimate: 14.42 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Net I/σ(I): 18.21
Reflection shellResolution: 1.5→1.6 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.657 / Mean I/σ(I) obs: 3.36 / Num. unique obs: 7965 / CC1/2: 0.902 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Y7A

6y7a


Resolution: 1.5→41.25 Å / SU ML: 0.181 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.6079
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1919 2306 5 %
Rwork0.162 43814 -
obs0.1635 46120 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.08 Å2
Refinement stepCycle: LAST / Resolution: 1.5→41.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2350 0 72 297 2719
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01272516
X-RAY DIFFRACTIONf_angle_d1.22863438
X-RAY DIFFRACTIONf_chiral_restr0.0807359
X-RAY DIFFRACTIONf_plane_restr0.0109466
X-RAY DIFFRACTIONf_dihedral_angle_d9.2195375
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.530.39371420.3542709X-RAY DIFFRACTION99.79
1.53-1.570.28931410.2322674X-RAY DIFFRACTION99.93
1.57-1.610.23831410.19192689X-RAY DIFFRACTION99.89
1.61-1.650.23231430.18722705X-RAY DIFFRACTION99.89
1.65-1.70.24891420.1882705X-RAY DIFFRACTION99.93
1.7-1.750.23231410.17382686X-RAY DIFFRACTION100
1.75-1.820.20311430.16192704X-RAY DIFFRACTION99.96
1.82-1.890.20851430.14342719X-RAY DIFFRACTION99.86
1.89-1.980.16331430.15072714X-RAY DIFFRACTION100
1.98-2.080.17381430.1552728X-RAY DIFFRACTION99.93
2.08-2.210.19311450.15272741X-RAY DIFFRACTION100
2.21-2.380.1721430.15282730X-RAY DIFFRACTION100
2.38-2.620.16551460.15932770X-RAY DIFFRACTION99.93
2.62-30.17551460.15982771X-RAY DIFFRACTION99.93
3-3.780.18171480.15232808X-RAY DIFFRACTION99.9
3.78-41.250.18121560.15172961X-RAY DIFFRACTION99.87

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