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

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Basic information

Entry
Database: PDB / ID: 7ziy
TitleX-ray structure of the haloalkane dehalogenase HaloTag7 bound to a pentyltrifluoromethanesulfonamide tetramethylrhodamine ligand (TMR-T5)
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
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-IYI / Haloalkane dehalogenase
Similarity search - Component
Biological speciesRhodococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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
B: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0046
Polymers66,4522
Non-polymers1,5524
Water4,882271
1
A: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0023
Polymers33,2261
Non-polymers7762
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0023
Polymers33,2261
Non-polymers7762
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.240, 46.060, 79.060
Angle α, β, γ (deg.)94.414, 90.000, 109.505
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-IYI / [9-[2-carboxy-5-[2-[2-[5-(trifluoromethylsulfonylamino)pentoxy]ethoxy]ethylcarbamoyl]phenyl]-6-(dimethylamino)xanthen-3-ylidene]-dimethyl-azanium


Mass: 735.790 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C35H42F3N4O8S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / 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: 45.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MES pH 6.0, 0.2 M calcium acetate, 21% (m/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99996 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 23, 2021
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99996 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 59538 / % possible obs: 92.3 % / Redundancy: 1.82 % / Biso Wilson estimate: 19.22 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.036 / Net I/σ(I): 12.25
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 1.76 % / Rmerge(I) obs: 0.234 / Mean I/σ(I) obs: 3 / Num. unique obs: 8598 / CC1/2: 0.906 / % possible all: 84.7

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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: 1.7→39.4 Å / SU ML: 0.2117 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 25.0978
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2243 2977 5 %
Rwork0.191 56558 -
obs0.1927 59535 92.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.65 Å2
Refinement stepCycle: LAST / Resolution: 1.7→39.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4700 0 104 271 5075
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01254984
X-RAY DIFFRACTIONf_angle_d1.22646830
X-RAY DIFFRACTIONf_chiral_restr0.0756716
X-RAY DIFFRACTIONf_plane_restr0.0105950
X-RAY DIFFRACTIONf_dihedral_angle_d5.544724
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.730.37171100.2892090X-RAY DIFFRACTION72.73
1.73-1.760.31941370.25452605X-RAY DIFFRACTION88.71
1.76-1.790.29811380.2232627X-RAY DIFFRACTION90.6
1.79-1.820.26951410.2052682X-RAY DIFFRACTION92.1
1.82-1.860.22041440.19922732X-RAY DIFFRACTION93.04
1.86-1.90.26041420.19982706X-RAY DIFFRACTION93.93
1.9-1.950.25091450.19362746X-RAY DIFFRACTION92.87
1.95-1.990.2191430.19132726X-RAY DIFFRACTION92.97
1.99-2.050.25041440.19772718X-RAY DIFFRACTION93.5
2.05-2.110.24191440.19342750X-RAY DIFFRACTION93.42
2.11-2.180.24011420.19172690X-RAY DIFFRACTION92.58
2.18-2.250.23961420.19322702X-RAY DIFFRACTION93.25
2.25-2.340.22121450.19742749X-RAY DIFFRACTION94.27
2.35-2.450.22051460.20062787X-RAY DIFFRACTION94.49
2.45-2.580.25971440.20012723X-RAY DIFFRACTION94.03
2.58-2.740.22941450.20522764X-RAY DIFFRACTION94.17
2.74-2.950.27331450.20332751X-RAY DIFFRACTION94.76
2.95-3.250.2261440.19612730X-RAY DIFFRACTION93.43
3.25-3.720.20271450.18742765X-RAY DIFFRACTION94.57
3.72-4.690.18171450.16012747X-RAY DIFFRACTION94.39
4.69-39.40.17331460.16872768X-RAY DIFFRACTION94.89

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