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

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Basic information

Entry
Database: PDB / ID: 7zix
TitleX-ray structure of the haloalkane dehalogenase HaloTag7 bound to a butylmethanesulfonamide tetramethylrhodamine ligand (TMR-S4)
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-IYU / Haloalkane dehalogenase
Similarity search - Component
Biological speciesRhodococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 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 HaloTag7 bound to a butylmethanesulfonamide tetramethylrhodamine ligand (HSAm(4)-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
B: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7884
Polymers66,4522
Non-polymers1,3362
Water2,612145
1
A: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8942
Polymers33,2261
Non-polymers6681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8942
Polymers33,2261
Non-polymers6681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.227, 78.399, 81.623
Angle α, β, γ (deg.)90.000, 92.571, 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.: 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-IYU / [9-[2-carboxy-5-[2-[2-[4-(methylsulfonylamino)butoxy]ethoxy]ethylcarbamoyl]phenyl]-6-(dimethylamino)xanthen-3-ylidene]-dimethyl-azanium


Mass: 667.792 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H43N4O8S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.13 Å3/Da / Density % sol: 42.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MES pH 6.0, 1.0 M lithium chloride, 23% (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: 1.00007 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 16, 2020
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00007 Å / Relative weight: 1
ReflectionResolution: 2.39→50 Å / Num. obs: 20776 / % possible obs: 93.5 % / Redundancy: 3.83 % / Biso Wilson estimate: 15.93 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.123 / Net I/σ(I): 7.5
Reflection shellResolution: 2.39→2.45 Å / Redundancy: 3.69 % / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 1039 / CC1/2: 0.874 / % possible all: 68.5

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
STARANISOdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Y7A

6y7a


Resolution: 2.39→44.18 Å / SU ML: 0.2158 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.5197
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2223 1074 5.18 %
Rwork0.197 19667 -
obs0.1983 20741 93.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.02 Å2
Refinement stepCycle: LAST / Resolution: 2.39→44.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4700 0 94 145 4939
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00344958
X-RAY DIFFRACTIONf_angle_d0.6256784
X-RAY DIFFRACTIONf_chiral_restr0.0461708
X-RAY DIFFRACTIONf_plane_restr0.006952
X-RAY DIFFRACTIONf_dihedral_angle_d12.79711858
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.39-2.50.2681950.26711882X-RAY DIFFRACTION71.97
2.5-2.630.27081260.25492218X-RAY DIFFRACTION84.26
2.63-2.790.25871450.23682444X-RAY DIFFRACTION93.4
2.79-3.010.22131330.22422576X-RAY DIFFRACTION98.69
3.01-3.310.23451410.20022613X-RAY DIFFRACTION99.64
3.31-3.790.24251380.18252633X-RAY DIFFRACTION99.6
3.79-4.770.17321550.15732632X-RAY DIFFRACTION99.82
4.78-44.180.19661410.16352669X-RAY DIFFRACTION99.05

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