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

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Basic information

Entry
Database: PDB / ID: 6zvx
TitleX-RAY STRUCTURE OF THE HALOALKANE DEHALOGENASE HALOTAG7-Q165H-P174L 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: To Be Published
Title: X-RAY STRUCTURE OF THE HALOALKANE DEHALOGENASE HALOTAG7-Q165H-P174L LABELED WITH A CHLOROALKANE-TETRAMETHYLRHODAMINE FLUOROPHORE SUBSTRATE
Authors: Tarnawski, M. / Frei, M. / Hiblot, J. / Johnsson, K.
History
DepositionJul 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)34,0174
Polymers33,2521
Non-polymers7653
Water6,413356
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint-14 kcal/mol
Surface area11440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.150, 78.210, 44.530
Angle α, β, γ (deg.)90.000, 118.462, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Haloalkane dehalogenase


Mass: 33252.043 Da / Num. of mol.: 1
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.: 1 / Source method: obtained synthetically / Formula: C35H43ClN3O6 / 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.: 356 / 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: 2.03 Å3/Da / Density % sol: 39.49 %
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: 50930 / % possible obs: 97.1 % / Redundancy: 3.44 % / Biso Wilson estimate: 9.34 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.028 / Net I/σ(I): 28.16
Reflection shellResolution: 1.4→1.5 Å / Redundancy: 2.66 % / Rmerge(I) obs: 0.094 / Mean I/σ(I) obs: 9.84 / Num. unique obs: 8653 / CC1/2: 0.985 / % possible all: 88.6

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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→39.15 Å / SU ML: 0.0977 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 15.3008
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1593 2547 5 %
Rwork0.1401 48383 -
obs0.1411 50930 97.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 12.38 Å2
Refinement stepCycle: LAST / Resolution: 1.4→39.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2352 0 51 356 2759
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00552514
X-RAY DIFFRACTIONf_angle_d0.88593445
X-RAY DIFFRACTIONf_chiral_restr0.0828362
X-RAY DIFFRACTIONf_plane_restr0.0082482
X-RAY DIFFRACTIONf_dihedral_angle_d5.42781508
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.430.18631160.16292196X-RAY DIFFRACTION79.45
1.43-1.460.20571270.15142410X-RAY DIFFRACTION87.97
1.46-1.490.18841370.14962622X-RAY DIFFRACTION96.03
1.49-1.520.15411450.14312747X-RAY DIFFRACTION98.27
1.52-1.560.14471410.14082675X-RAY DIFFRACTION98.7
1.56-1.60.16751440.13312739X-RAY DIFFRACTION99.21
1.6-1.650.17331440.13672741X-RAY DIFFRACTION99.41
1.65-1.70.14121440.13112729X-RAY DIFFRACTION99.14
1.7-1.760.1751440.13752736X-RAY DIFFRACTION99.41
1.76-1.830.17171440.13882735X-RAY DIFFRACTION99.58
1.83-1.920.15221440.13642740X-RAY DIFFRACTION99.14
1.92-2.020.15491440.13572735X-RAY DIFFRACTION99.65
2.02-2.150.15131440.13592739X-RAY DIFFRACTION99.31
2.15-2.310.17571450.14372752X-RAY DIFFRACTION99.35
2.31-2.540.15541440.14512738X-RAY DIFFRACTION99.59
2.54-2.910.1921460.15232781X-RAY DIFFRACTION99.59
2.91-3.670.13761452749X-RAY DIFFRACTION99.59
3.67-39.150.14451490.13262819X-RAY DIFFRACTION99.8

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