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- PDB-7ziv: X-ray structure of the haloalkane dehalogenase dead variant HaloT... -

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Basic information

Entry
Database: PDB / ID: 7ziv
TitleX-ray structure of the haloalkane dehalogenase dead variant HaloTag7-D106A bound to a chloroalkane tetramethylrhodamine fluorophore ligand (CA-TMR)
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 / 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. / Kompa, J. / Johnsson, K. / Hiblot, J.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: To Be Published
Title: X-ray structure of the haloalkane dehalogenase dead variant HaloTag7-D106A bound to a chloroalkane tetramethylrhodamine fluorophore ligand (CA-TMR)
Authors: Tarnawski, M. / Kompa, J. / Johnsson, K. / Hiblot, J.
History
DepositionApr 8, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 19, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9474
Polymers33,1821
Non-polymers7653
Water3,351186
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.010, 77.350, 44.290
Angle α, β, γ (deg.)90.000, 118.525, 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: 33181.973 Da / Num. of mol.: 1 / Mutation: D106A
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.: 186 / 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 Å3/Da / Density % sol: 38.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MES pH 6.0, 1.0 M lithium chloride, 18% (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: 0.99985 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 2, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99985 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 48314 / % possible obs: 93.9 % / Redundancy: 2.72 % / Biso Wilson estimate: 13.16 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.061 / Net I/σ(I): 10.56
Reflection shellResolution: 1.4→1.5 Å / Redundancy: 2.17 % / Rmerge(I) obs: 0.378 / Mean I/σ(I) obs: 2.72 / Num. unique obs: 7989 / CC1/2: 0.801 / % possible all: 83.4

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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: 1.4→38.67 Å / SU ML: 0.1616 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.6716
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.195 2414 5 %
Rwork0.1712 45891 -
obs0.1724 48305 94.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.08 Å2
Refinement stepCycle: LAST / Resolution: 1.4→38.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2347 0 52 186 2585
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01532551
X-RAY DIFFRACTIONf_angle_d1.3853493
X-RAY DIFFRACTIONf_chiral_restr0.1106358
X-RAY DIFFRACTIONf_plane_restr0.013521
X-RAY DIFFRACTIONf_dihedral_angle_d6.3316408
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.430.29061090.24812076X-RAY DIFFRACTION72.69
1.43-1.460.2851260.23542403X-RAY DIFFRACTION83.69
1.46-1.490.25611380.20732623X-RAY DIFFRACTION92.46
1.49-1.530.24691420.19562703X-RAY DIFFRACTION94.8
1.53-1.570.18961460.17942772X-RAY DIFFRACTION96.53
1.57-1.620.20461470.17672784X-RAY DIFFRACTION97.09
1.62-1.670.23571420.16952712X-RAY DIFFRACTION95.97
1.67-1.730.22411490.17222817X-RAY DIFFRACTION98.21
1.73-1.80.21531470.16692800X-RAY DIFFRACTION98.27
1.8-1.880.21421470.16872804X-RAY DIFFRACTION98.24
1.88-1.980.18971470.15462785X-RAY DIFFRACTION96.54
1.98-2.110.1941460.15412777X-RAY DIFFRACTION97.3
2.11-2.270.17471460.16362763X-RAY DIFFRACTION96.81
2.27-2.50.19441440.17242750X-RAY DIFFRACTION95.83
2.5-2.860.18681460.17942764X-RAY DIFFRACTION96.39
2.86-3.60.18721430.17052734X-RAY DIFFRACTION94.61
3.6-38.670.17061490.16272824X-RAY DIFFRACTION96.46

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