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- PDB-6y7a: X-ray structure of the Haloalkane dehalogenase HaloTag7 labeled w... -

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Basic information

Entry
Database: PDB / ID: 6y7a
TitleX-ray structure of the Haloalkane dehalogenase HaloTag7 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 / 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-OEH / Haloalkane dehalogenase
Similarity search - Component
Biological speciesRhodococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsTarnawski, M. / Johnsson, K. / Hiblot, J.
Citation
Journal: Biochemistry / Year: 2021
Title: Kinetic and Structural Characterization of the Self-Labeling Protein Tags HaloTag7, SNAP-tag, and CLIP-tag.
Authors: Wilhelm, J. / Kuhn, S. / Tarnawski, M. / Gotthard, G. / Tunnermann, J. / Tanzer, T. / Karpenko, J. / Mertes, N. / Xue, L. / Uhrig, U. / Reinstein, J. / Hiblot, J. / Johnsson, K.
#1: Journal: Biorxiv / Year: 2021
Title: Kinetic and structural characterization of the self-labeling protein tags HaloTag7, SNAP-tag and CLIP-tag
Authors: Wilhelm, J. / Kuhn, S. / Tarnawski, M. / Gotthard, G. / Tunnermann, J. / Tanzer, T. / Karpenko, J. / Mertes, N. / Xue, L. / Uhrig, U. / Reinstein, J. / Hiblot, J. / Johnsson, K.
History
DepositionFeb 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 27, 2021Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_database_proc / struct
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct.title
Revision 1.2Nov 10, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)33,9914
Polymers33,2261
Non-polymers7653
Water6,269348
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area430 Å2
ΔGint-13 kcal/mol
Surface area11270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.000, 78.140, 45.240
Angle α, β, γ (deg.)90.000, 119.966, 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: 33225.980 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.: 348 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 39.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MES pH 6.0, 1.0 M lithium chloride, 15% (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: 1.00001 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 17, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 50448 / % possible obs: 96.5 % / Redundancy: 3.18 % / Biso Wilson estimate: 13.58 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.063 / Net I/σ(I): 9.59
Reflection shellResolution: 1.4→1.5 Å / Redundancy: 3.17 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.83 / Num. unique obs: 9451 / CC1/2: 0.864 / % possible all: 97.1

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UY1

5uy1


Resolution: 1.4→39.19 Å / SU ML: 0.1374 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.3697
RfactorNum. reflection% reflection
Rfree0.1868 2523 5 %
Rwork0.1558 --
obs0.1573 50435 96.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 18.93 Å2
Refinement stepCycle: LAST / Resolution: 1.4→39.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2350 0 51 348 2749
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01272537
X-RAY DIFFRACTIONf_angle_d1.24663482
X-RAY DIFFRACTIONf_chiral_restr0.1029365
X-RAY DIFFRACTIONf_plane_restr0.011490
X-RAY DIFFRACTIONf_dihedral_angle_d5.57321520
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.430.25821410.23792667X-RAY DIFFRACTION97.36
1.43-1.460.27951400.23572673X-RAY DIFFRACTION97.4
1.46-1.490.28341400.21372645X-RAY DIFFRACTION97.38
1.49-1.520.2551410.20662678X-RAY DIFFRACTION96.87
1.52-1.560.25021400.18742665X-RAY DIFFRACTION97.19
1.56-1.60.23741400.19162655X-RAY DIFFRACTION97.08
1.6-1.650.20851390.18352645X-RAY DIFFRACTION96.87
1.65-1.70.22661400.17382661X-RAY DIFFRACTION96.45
1.7-1.760.17781390.17022629X-RAY DIFFRACTION95.75
1.76-1.830.20621380.16732622X-RAY DIFFRACTION95.73
1.83-1.920.21561380.15752625X-RAY DIFFRACTION95.44
1.92-2.020.2121380.15922624X-RAY DIFFRACTION95.97
2.02-2.150.181390.15282639X-RAY DIFFRACTION95.63
2.15-2.310.18111380.14952621X-RAY DIFFRACTION95.14
2.31-2.540.17511390.15772653X-RAY DIFFRACTION96.61
2.54-2.910.1871440.15412720X-RAY DIFFRACTION98.12
2.91-3.670.16961420.13152703X-RAY DIFFRACTION98
3.67-39.190.14171470.13232787X-RAY DIFFRACTION98.95

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