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- PDB-6zvy: X-RAY STRUCTURE OF THE HALOALKANE DEHALOGENASE HALOTAG7-Q165H-P17... -

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Basic information

Entry
Database: PDB / ID: 6zvy
TitleX-RAY STRUCTURE OF THE HALOALKANE DEHALOGENASE HALOTAG7-Q165H-P174R LABELED WITH A CHLOROALKANE-TETRAMETHYLRHODAMINE FLUOROPHORE SUBSTRATE
ComponentsHaloalkane dehalogenase
KeywordsHYDROLASE / HALOALKANE DEHALOGENASE / HALO / TAG / 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-OEH / Haloalkane dehalogenase
Similarity search - Component
Biological speciesRhodococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsTarnawski, M. / Frei, M. / Hiblot, J. / Johnsson, K.
CitationJournal: Nat.Methods / Year: 2022
Title: Engineered HaloTag variants for fluorescence lifetime multiplexing.
Authors: Frei, M.S. / Tarnawski, M. / Roberti, M.J. / Koch, B. / Hiblot, J. / Johnsson, K.
History
DepositionJul 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 31, 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)68,30610
Polymers66,5922
Non-polymers1,7148
Water11,674648
1
A: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1535
Polymers33,2961
Non-polymers8574
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1535
Polymers33,2961
Non-polymers8574
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.150, 47.340, 78.470
Angle α, β, γ (deg.)97.667, 90.193, 113.538
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: 33296.078 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-OEH / [9-[2-carboxy-5-[2-[2-(6-chloranylhexoxy)ethoxy]ethylcarbamoyl]phenyl]-6-(dimethylamino)xanthen-3-ylidene]-dimethyl-azanium


Mass: 637.185 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C35H43ClN3O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 648 / 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: 2.23 Å3/Da / Density % sol: 44.93 %
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: 0.999878 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 12, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999878 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 99388 / % possible obs: 87.5 % / Redundancy: 1.91 % / Biso Wilson estimate: 13.43 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.026 / Net I/σ(I): 17.82
Reflection shellResolution: 1.4→1.5 Å / Redundancy: 1.81 % / Rmerge(I) obs: 0.125 / Mean I/σ(I) obs: 5.57 / Num. unique obs: 14156 / CC1/2: 0.971 / % possible all: 66.7

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Y7A

6y7a


Resolution: 1.4→40.4 Å / SU ML: 0.1237 / Cross valid method: FREE R-VALUE / σ(F): 2.02 / Phase error: 19.8836
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.18 4970 5 %
Rwork0.1621 94409 -
obs0.163 99379 87.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.92 Å2
Refinement stepCycle: LAST / Resolution: 1.4→40.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4710 0 114 648 5472
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00565006
X-RAY DIFFRACTIONf_angle_d0.88166842
X-RAY DIFFRACTIONf_chiral_restr0.0813714
X-RAY DIFFRACTIONf_plane_restr0.0076956
X-RAY DIFFRACTIONf_dihedral_angle_d7.81943018
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.2354920.18171738X-RAY DIFFRACTION48.64
1.42-1.430.2051030.18781958X-RAY DIFFRACTION53.76
1.43-1.450.25241150.18162182X-RAY DIFFRACTION61.34
1.45-1.470.21011360.18462589X-RAY DIFFRACTION71.3
1.47-1.490.22321600.17613034X-RAY DIFFRACTION85.01
1.49-1.510.21680.17043204X-RAY DIFFRACTION89.3
1.51-1.530.22651760.16333331X-RAY DIFFRACTION91.33
1.53-1.550.19141700.16773242X-RAY DIFFRACTION92.24
1.55-1.580.1961790.16513392X-RAY DIFFRACTION92.83
1.58-1.60.20421720.16553276X-RAY DIFFRACTION92.51
1.6-1.630.19171770.1653352X-RAY DIFFRACTION91.83
1.63-1.660.20691710.16143259X-RAY DIFFRACTION92.43
1.66-1.690.19791770.16123370X-RAY DIFFRACTION92.35
1.69-1.730.17911740.15813306X-RAY DIFFRACTION92.43
1.73-1.760.18291750.15943321X-RAY DIFFRACTION92.32
1.76-1.80.1751740.16663295X-RAY DIFFRACTION92.16
1.8-1.850.19311720.17473279X-RAY DIFFRACTION91.15
1.85-1.90.21791750.17383326X-RAY DIFFRACTION91.89
1.9-1.960.18691720.16683266X-RAY DIFFRACTION91.24
1.96-2.020.17171730.1613275X-RAY DIFFRACTION91.14
2.02-2.090.18971740.16283318X-RAY DIFFRACTION91.56
2.09-2.170.19271720.16493273X-RAY DIFFRACTION91.28
2.17-2.270.17111740.16123292X-RAY DIFFRACTION92.13
2.27-2.390.20411750.16763320X-RAY DIFFRACTION92.17
2.39-2.540.16041723287X-RAY DIFFRACTION91.68
2.54-2.740.18181760.16993340X-RAY DIFFRACTION92.84
2.74-3.020.18711770.17213357X-RAY DIFFRACTION93.22
3.02-3.450.16171780.15053378X-RAY DIFFRACTION94.2
3.45-4.350.15521800.14443432X-RAY DIFFRACTION94.93
4.35-40.40.16031810.15713417X-RAY DIFFRACTION95.31

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