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- PDB-8b6s: X-ray structure of the haloalkane dehalogenase HaloTag7 fusion to... -

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Basic information

Entry
Database: PDB / ID: 8b6s
TitleX-ray structure of the haloalkane dehalogenase HaloTag7 fusion to the green fluorescent protein GFP (ChemoG1) labeled with a chloroalkane tetramethylrhodamine fluorophore substrate
ComponentsGreen fluorescent protein,Haloalkane dehalogenase
KeywordsHYDROLASE / haloalkane dehalogenase / HaloTag / HaloTag7 / Self-Labeling Protein / green fluorescent protein / GFP / fluorophore / tetramethylerhodamine / TMR
Function / homology
Function and homology information


haloalkane dehalogenase / haloalkane dehalogenase activity / bioluminescence / generation of precursor metabolites and energy / response to toxic substance / membrane
Similarity search - Function
Haloalkane dehalogenase, subfamily 2 / : / Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Alpha/Beta hydrolase fold, catalytic domain ...Haloalkane dehalogenase, subfamily 2 / : / Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / 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 / Green fluorescent protein
Similarity search - Component
Biological speciesRhodococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsTarnawski, M. / Hellweg, L. / Hiblot, J.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Nat.Chem.Biol. / Year: 2023
Title: A general method for the development of multicolor biosensors with large dynamic ranges.
Authors: Hellweg, L. / Edenhofer, A. / Barck, L. / Huppertz, M.C. / Frei, M.S. / Tarnawski, M. / Bergner, A. / Koch, B. / Johnsson, K. / Hiblot, J.
History
DepositionSep 27, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Nov 13, 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: Green fluorescent protein,Haloalkane dehalogenase
B: Green fluorescent protein,Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,5118
Polymers119,9822
Non-polymers1,5296
Water8,287460
1
A: Green fluorescent protein,Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7564
Polymers59,9911
Non-polymers7653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Green fluorescent protein,Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7564
Polymers59,9911
Non-polymers7653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.190, 63.710, 89.420
Angle α, β, γ (deg.)93.561, 91.015, 90.850
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 Green fluorescent protein,Haloalkane dehalogenase


Mass: 59990.988 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus sp. (bacteria) / Gene: GFP, dhaA / Production host: Escherichia coli (E. coli)
References: UniProt: P42212, 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


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 460 / 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: 2.19 Å3/Da / Density % sol: 43.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.085 M Tris-HCl pH 8.5, 0.17 M sodium acetate, 15% (v/v) glycerol, 27% (m/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99996 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 23, 2021
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99996 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 89852 / % possible obs: 95.3 % / Redundancy: 2 % / Biso Wilson estimate: 24.95 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.041 / Net I/σ(I): 11.99
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 2 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.12 / Num. unique obs: 13310 / CC1/2: 0.752 / % possible all: 94.3

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Y2X, 1GFL

5y2x

1gfl


Resolution: 1.8→46.18 Å / SU ML: 0.2232 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 20.5292
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2008 4492 5 %
Rwork0.1728 85350 -
obs0.1742 89842 95.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.13 Å2
Refinement stepCycle: LAST / Resolution: 1.8→46.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8305 0 102 460 8867
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00668664
X-RAY DIFFRACTIONf_angle_d1.093711793
X-RAY DIFFRACTIONf_chiral_restr0.06011250
X-RAY DIFFRACTIONf_plane_restr0.00771602
X-RAY DIFFRACTIONf_dihedral_angle_d13.22733221
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.36451500.32642854X-RAY DIFFRACTION94.79
1.82-1.840.35221470.29922796X-RAY DIFFRACTION94.03
1.84-1.860.29431470.27362796X-RAY DIFFRACTION94.27
1.86-1.890.29051500.23492835X-RAY DIFFRACTION94.43
1.89-1.910.21391470.20742811X-RAY DIFFRACTION94.29
1.91-1.940.23491470.19642807X-RAY DIFFRACTION93.81
1.94-1.970.23151470.18462779X-RAY DIFFRACTION94.54
1.97-20.22571510.18572881X-RAY DIFFRACTION94.16
2-2.030.21971480.18562816X-RAY DIFFRACTION95.15
2.03-2.060.21151490.18352824X-RAY DIFFRACTION95.41
2.06-2.10.20821490.18492837X-RAY DIFFRACTION94.11
2.1-2.130.23061520.18212874X-RAY DIFFRACTION96.09
2.13-2.180.20821500.17762852X-RAY DIFFRACTION95.57
2.18-2.220.23191480.17532822X-RAY DIFFRACTION95.35
2.22-2.270.22351510.17292861X-RAY DIFFRACTION95.35
2.27-2.320.20721490.17422827X-RAY DIFFRACTION94.63
2.32-2.380.21451480.17862818X-RAY DIFFRACTION95.74
2.38-2.440.21961520.17982886X-RAY DIFFRACTION95.15
2.44-2.510.25281470.18332785X-RAY DIFFRACTION94.64
2.51-2.60.20741510.18262873X-RAY DIFFRACTION95.21
2.6-2.690.20671490.18362829X-RAY DIFFRACTION95.24
2.69-2.80.21751510.18712880X-RAY DIFFRACTION96.25
2.8-2.920.23011510.18582875X-RAY DIFFRACTION96.34
2.92-3.080.19521520.18052882X-RAY DIFFRACTION95.83
3.08-3.270.21351510.16892860X-RAY DIFFRACTION96.38
3.27-3.520.18171510.16852880X-RAY DIFFRACTION96.5
3.52-3.880.17831510.16242870X-RAY DIFFRACTION95.9
3.88-4.440.16491520.13742877X-RAY DIFFRACTION96.93
4.44-5.590.14491520.14032890X-RAY DIFFRACTION95.99
5.59-46.180.1751520.1542873X-RAY DIFFRACTION96.77

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