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- PDB-7zj0: X-ray structure of the haloalkane dehalogenase HaloTag7 bound to ... -

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Basic information

Entry
Database: PDB / ID: 7zj0
TitleX-ray structure of the haloalkane dehalogenase HaloTag7 bound to a pentylmethanesulfonamide tetramethylrhodamine ligand (TMR-S5)
ComponentsHaloalkane dehalogenase
KeywordsHYDROLASE / haloalkane dehalogenase / HaloTag / HaloTag7 / Self-Labeling Protein / Fluorophore / Tetramethylrhodamine
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-IYO / Haloalkane dehalogenase
Similarity search - Component
Biological speciesRhodococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsTarnawski, M. / Kompa, J. / Johnsson, K. / Hiblot, J.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: J.Am.Chem.Soc. / Year: 2023
Title: Exchangeable HaloTag Ligands for Super-Resolution Fluorescence Microscopy.
Authors: Kompa, J. / Bruins, J. / Glogger, M. / Wilhelm, J. / Frei, M.S. / Tarnawski, M. / D'Este, E. / Heilemann, M. / Hiblot, J. / Johnsson, K.
History
DepositionApr 8, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)68,36810
Polymers66,4522
Non-polymers1,9168
Water7,512417
1
A: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2766
Polymers33,2261
Non-polymers1,0505
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0924
Polymers33,2261
Non-polymers8663
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.290, 49.930, 78.720
Angle α, β, γ (deg.)71.230, 89.906, 67.810
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein Haloalkane dehalogenase


Mass: 33225.980 Da / Num. of mol.: 2
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
#2: Chemical ChemComp-IYO / [9-[2-carboxy-5-[2-[2-[5-(methylsulfonylamino)pentoxy]ethoxy]ethylcarbamoyl]phenyl]-6-(dimethylamino)xanthen-3-ylidene]-dimethyl-azanium


Mass: 681.819 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C35H45N4O8S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 417 / Source method: isolated from a natural source / Formula: H2O
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: 2.28 Å3/Da / Density % sol: 45.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MES pH 6.0, 1.0 M lithium chloride, 20% (m/v) PEG 6000

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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: 85890 / % possible obs: 91.4 % / Redundancy: 1.93 % / Biso Wilson estimate: 16.69 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.039 / Net I/σ(I): 11.8
Reflection shellResolution: 1.5→1.6 Å / Redundancy: 1.99 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 2.51 / Num. unique obs: 14710 / CC1/2: 0.77 / % possible all: 88.6

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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→43.36 Å / SU ML: 0.1916 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 23.5251
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2052 4295 5 %
Rwork0.1747 81591 -
obs0.1762 85886 91.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.92 Å2
Refinement stepCycle: LAST / Resolution: 1.5→43.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4700 0 132 417 5249
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01335024
X-RAY DIFFRACTIONf_angle_d1.26386873
X-RAY DIFFRACTIONf_chiral_restr0.0794715
X-RAY DIFFRACTIONf_plane_restr0.0127962
X-RAY DIFFRACTIONf_dihedral_angle_d6.2978740
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.36481410.33422674X-RAY DIFFRACTION89.03
1.52-1.530.33721360.29112580X-RAY DIFFRACTION88.01
1.53-1.550.33671370.26782614X-RAY DIFFRACTION88.37
1.55-1.570.32761410.23692667X-RAY DIFFRACTION88.69
1.57-1.590.23891380.232626X-RAY DIFFRACTION89.02
1.59-1.620.28971380.23472634X-RAY DIFFRACTION88.36
1.62-1.640.25431410.22272678X-RAY DIFFRACTION89.29
1.64-1.660.29661390.22992635X-RAY DIFFRACTION89.74
1.66-1.690.28251410.22862673X-RAY DIFFRACTION90.34
1.69-1.720.24091440.20312751X-RAY DIFFRACTION90.95
1.72-1.750.23641400.19692645X-RAY DIFFRACTION89.84
1.75-1.780.23421430.18342714X-RAY DIFFRACTION90.64
1.78-1.810.22121410.17192686X-RAY DIFFRACTION91.46
1.81-1.850.21711440.17232740X-RAY DIFFRACTION91.09
1.85-1.890.21991400.17162658X-RAY DIFFRACTION91.38
1.89-1.930.20271440.16512735X-RAY DIFFRACTION90.88
1.93-1.980.22661430.17392714X-RAY DIFFRACTION91.86
1.98-2.040.20021430.17692713X-RAY DIFFRACTION91.54
2.04-2.10.2271470.17932807X-RAY DIFFRACTION93.57
2.1-2.160.19611460.16882760X-RAY DIFFRACTION93.41
2.16-2.240.17771480.16662824X-RAY DIFFRACTION94.23
2.24-2.330.2181470.17072792X-RAY DIFFRACTION94.59
2.33-2.440.20441460.17652768X-RAY DIFFRACTION93.22
2.44-2.560.22561430.17592726X-RAY DIFFRACTION92.16
2.56-2.730.21541460.17832773X-RAY DIFFRACTION92.9
2.73-2.940.22311480.18032808X-RAY DIFFRACTION93.81
2.94-3.230.19051460.1712772X-RAY DIFFRACTION94.25
3.23-3.70.1661480.16172809X-RAY DIFFRACTION94.38
3.7-4.660.15261470.13662802X-RAY DIFFRACTION94.4
4.66-43.360.16841490.15432813X-RAY DIFFRACTION94.36

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