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- PDB-7zbd: HaloTag with TRaQ-G ligand -

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Basic information

Entry
Database: PDB / ID: 7zbd
TitleHaloTag with TRaQ-G ligand
ComponentsHaloalkane dehalogenase
KeywordsHYDROLASE / HaloTag / haloalkane dehalogenase / silicon rhodamine
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-ILQ / Chem-ILU / Haloalkane dehalogenase
Similarity search - Component
Biological speciesRhodococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsEmmert, S. / Rivera-Fuentes, P. / Pojer, F. / Lau, K.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science FoundationPCEGP2_186862 Switzerland
Citation
Journal: Nat.Chem. / Year: 2023
Title: A locally activatable sensor for robust quantification of organellar glutathione.
Authors: Emmert, S. / Quargnali, G. / Thallmair, S. / Rivera-Fuentes, P.
#1: Journal: Biorxiv / Year: 2022
Title: A Locally Activatable Sensor for Robust Quantification of Organellar Glutathione
Authors: Hubner, S. / Quargnali, G. / Thallmair, S. / Rivera-Fuentes, P.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#3: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionMar 23, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2023Group: Database references / Category: citation / citation_author
Revision 1.2Jul 19, 2023Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.name / _citation_author.identifier_ORCID
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Feb 7, 2024Group: Refinement description / Category: 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)70,5238
Polymers68,9472
Non-polymers1,5776
Water7,819434
1
A: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2614
Polymers34,4731
Non-polymers7883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2624
Polymers34,4731
Non-polymers7893
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)166.905, 50.460, 79.476
Angle α, β, γ (deg.)90.000, 117.740, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11B-697-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Haloalkane dehalogenase /


Mass: 34473.312 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 BL21(DE3) (bacteria) / References: UniProt: P0A3G3, haloalkane dehalogenase

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Non-polymers , 5 types, 440 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ILQ / (10R)-7-azanyl-N-[2-[2-(6-chloranylhexoxy)ethoxy]ethyl]-2'-cyano-5,5-dimethyl-3-(methylamino)-1'-oxidanylidene-spiro[benzo[b][1]benzosiline-10,3'-isoindole]-5'-carboxamide


Mass: 660.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H42ClN5O4Si / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-ILU / [7-azanyl-10-[5-[2-[2-(6-chloranylhexoxy)ethoxy]ethylcarbamoyl]-2-(cyanocarbamoyl)phenyl]-5,5-dimethyl-benzo[b][1]benzosilin-3-ylidene]-methyl-azanium


Mass: 661.286 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H43ClN5O4Si / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 434 / 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: 2.15 Å3/Da / Density % sol: 42.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 20% v/v PEG 6000, 10% ethylene glycol, 0.1M magnesium chloride hexahydrate and 0.1M MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.68→50 Å / Num. obs: 127898 / % possible obs: 98.4 % / Redundancy: 3 % / Biso Wilson estimate: 21.94 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.12 / Net I/σ(I): 7.24
Reflection shellResolution: 1.68→1.79 Å / Mean I/σ(I) obs: 0.98 / Num. unique obs: 20136 / CC1/2: 0.61 / Rrim(I) all: 1.2 / % possible all: 96.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHASER1.20.1_4487phasing
Cootmodel building
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6U32

6u32


Resolution: 1.68→47.75 Å / SU ML: 0.1983 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.0217
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2223 3301 5 %
Rwork0.1862 62694 -
obs0.188 65995 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.09 Å2
Refinement stepCycle: LAST / Resolution: 1.68→47.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4673 0 104 434 5211
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01174962
X-RAY DIFFRACTIONf_angle_d1.17296791
X-RAY DIFFRACTIONf_chiral_restr0.0738707
X-RAY DIFFRACTIONf_plane_restr0.0121883
X-RAY DIFFRACTIONf_dihedral_angle_d11.4487661
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.710.38331200.34942287X-RAY DIFFRACTION88.36
1.71-1.730.32241380.3262600X-RAY DIFFRACTION99.64
1.73-1.760.35331370.31512590X-RAY DIFFRACTION99.63
1.76-1.790.30641380.29252621X-RAY DIFFRACTION99.86
1.79-1.820.3031370.27912614X-RAY DIFFRACTION99.89
1.82-1.850.31561380.2682610X-RAY DIFFRACTION99.82
1.85-1.890.30941370.2562597X-RAY DIFFRACTION99.78
1.89-1.930.32651360.2592586X-RAY DIFFRACTION99.71
1.93-1.970.27851390.24082630X-RAY DIFFRACTION99.96
1.97-2.020.28181390.22632638X-RAY DIFFRACTION99.82
2.02-2.070.2221340.20352561X-RAY DIFFRACTION99.81
2.07-2.120.26171380.20182633X-RAY DIFFRACTION99.93
2.12-2.190.21841390.18262634X-RAY DIFFRACTION99.96
2.19-2.260.21791390.18392632X-RAY DIFFRACTION99.86
2.26-2.340.20941380.17772620X-RAY DIFFRACTION99.93
2.34-2.430.211380.17532623X-RAY DIFFRACTION99.96
2.43-2.540.23531380.1822619X-RAY DIFFRACTION99.86
2.54-2.670.25011390.1892651X-RAY DIFFRACTION99.96
2.67-2.840.21231380.18632630X-RAY DIFFRACTION99.75
2.84-3.060.20121390.18662625X-RAY DIFFRACTION99.86
3.06-3.370.20281400.17452666X-RAY DIFFRACTION99.96
3.37-3.860.22461380.15862627X-RAY DIFFRACTION99.6
3.86-4.860.16611410.13222673X-RAY DIFFRACTION99.79
4.86-47.750.1741430.1622727X-RAY DIFFRACTION98.83

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