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- PDB-7ziz: X-ray structure of the dead variant haloalkane dehalogenase HaloT... -

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Basic information

Entry
Database: PDB / ID: 7ziz
TitleX-ray structure of the dead variant haloalkane dehalogenase HaloTag7-D106A bound to a pentanol tetramethylrhodamine ligand (TMR-Hy5)
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-IYL / 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

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Assembly

Deposited unit
A: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9144
Polymers33,1821
Non-polymers7323
Water4,197233
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)77.830, 88.710, 44.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein Haloalkane dehalogenase


Mass: 33181.973 Da / Num. of mol.: 1 / Mutation: D106A
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-IYL / [9-[2-carboxy-5-[2-[2-(5-oxidanylpentoxy)ethoxy]ethylcarbamoyl]phenyl]-6-(dimethylamino)xanthen-3-ylidene]-dimethyl-azanium


Mass: 604.713 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H42N3O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 2.3 Å3/Da / Density % sol: 46.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MES pH 6.0, 1.0 M lithium chloride, 19% (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: 1.00008 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 21, 2021
RadiationMonochromator: si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00008 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 49719 / % possible obs: 99.8 % / Redundancy: 6.99 % / Biso Wilson estimate: 15.44 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.062 / Net I/σ(I): 18.66
Reflection shellResolution: 1.5→1.6 Å / Redundancy: 7.21 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 6.15 / Num. unique obs: 8612 / CC1/2: 0.971 / % possible all: 99.6

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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→44.35 Å / SU ML: 0.1786 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 18.9309
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1948 2486 5 %
Rwork0.1692 47228 -
obs0.1705 49714 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.52 Å2
Refinement stepCycle: LAST / Resolution: 1.5→44.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2347 0 51 233 2631
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01132493
X-RAY DIFFRACTIONf_angle_d1.18843410
X-RAY DIFFRACTIONf_chiral_restr0.0716356
X-RAY DIFFRACTIONf_plane_restr0.0122476
X-RAY DIFFRACTIONf_dihedral_angle_d5.5929362
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.530.35381360.32242594X-RAY DIFFRACTION99.64
1.53-1.560.28771350.24892553X-RAY DIFFRACTION99.48
1.56-1.590.22421360.20292597X-RAY DIFFRACTION99.6
1.59-1.630.23441360.18022569X-RAY DIFFRACTION99.56
1.63-1.670.21361350.15792574X-RAY DIFFRACTION99.78
1.67-1.720.19541370.16132606X-RAY DIFFRACTION99.78
1.72-1.770.20481380.16722623X-RAY DIFFRACTION99.82
1.77-1.820.21781360.18332576X-RAY DIFFRACTION99.85
1.82-1.890.24431370.18782600X-RAY DIFFRACTION99.89
1.89-1.970.2271370.16092613X-RAY DIFFRACTION100
1.97-2.050.17411370.15212602X-RAY DIFFRACTION99.89
2.06-2.160.1861390.16042636X-RAY DIFFRACTION100
2.16-2.30.19541380.16062627X-RAY DIFFRACTION99.82
2.3-2.480.17521390.16892634X-RAY DIFFRACTION99.86
2.48-2.730.18181390.17192646X-RAY DIFFRACTION100
2.73-3.120.19061410.1682670X-RAY DIFFRACTION99.82
3.12-3.930.18041410.15672677X-RAY DIFFRACTION99.68
3.93-44.350.1751490.1632831X-RAY DIFFRACTION99.73

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