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- PDB-7pcx: X-RAY STRUCTURE OF THE HALOALKANE DEHALOGENASE HALOTAG7-Q165W LAB... -

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Basic information

Entry
Database: PDB / ID: 7pcx
TitleX-RAY STRUCTURE OF THE HALOALKANE DEHALOGENASE HALOTAG7-Q165W 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.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat.Methods / Year: 2022
Title: Engineered HaloTag variants for fluorescence lifetime multiplexing.
Authors: Frei, M.S. / Tarnawski, M. / Roberti, M.J. / Koch, B. / Hiblot, J. / Johnsson, K.
History
DepositionAug 4, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 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

Downloads & links

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Assembly

Deposited unit
A: Haloalkane dehalogenase
B: Haloalkane dehalogenase
C: Haloalkane dehalogenase
D: Haloalkane dehalogenase
E: Haloalkane dehalogenase
F: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,38525
Polymers199,7046
Non-polymers4,68019
Water20,8791159
1
A: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0494
Polymers33,2841
Non-polymers7653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0494
Polymers33,2841
Non-polymers7653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0494
Polymers33,2841
Non-polymers7653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0494
Polymers33,2841
Non-polymers7653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1415
Polymers33,2841
Non-polymers8574
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0494
Polymers33,2841
Non-polymers7653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.960, 149.150, 79.920
Angle α, β, γ (deg.)90.000, 117.965, 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: 33284.062 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus sp. (bacteria) / Gene: dhaA / Production host: Escherichia coli BL21(DE3) (bacteria) / 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.: 6 / Source method: obtained synthetically / Formula: C35H43ClN3O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1159 / 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: 1.98 Å3/Da / Density % sol: 37.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MES pH 6.0, 1.0 M lithium chloride, 21% (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 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 26, 2021
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 300540 / % possible obs: 98.9 % / Redundancy: 3.42 % / Biso Wilson estimate: 11.72 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.031 / Net I/σ(I): 22.96
Reflection shellResolution: 1.4→1.5 Å / Redundancy: 3.31 % / Rmerge(I) obs: 0.206 / Mean I/σ(I) obs: 6.09 / Num. unique obs: 56041 / CC1/2: 0.957 / % possible all: 98.9

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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→39.86 Å / SU ML: 0.1687 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 18.4517
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1982 15024 5 %
Rwork0.1755 285456 -
obs0.1766 300480 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.43 Å2
Refinement stepCycle: LAST / Resolution: 1.4→39.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14130 0 312 1159 15601
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006215107
X-RAY DIFFRACTIONf_angle_d0.909720684
X-RAY DIFFRACTIONf_chiral_restr0.08382142
X-RAY DIFFRACTIONf_plane_restr0.00892925
X-RAY DIFFRACTIONf_dihedral_angle_d11.94015699
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.40314990.39979485X-RAY DIFFRACTION99.09
1.42-1.430.33384970.32539457X-RAY DIFFRACTION98.99
1.43-1.450.29165000.26349486X-RAY DIFFRACTION98.81
1.45-1.470.26515000.22639512X-RAY DIFFRACTION99.09
1.47-1.490.23914990.20499465X-RAY DIFFRACTION99.18
1.49-1.510.2335050.18529609X-RAY DIFFRACTION99.13
1.51-1.530.19624960.16929428X-RAY DIFFRACTION98.94
1.53-1.550.20485000.17059491X-RAY DIFFRACTION99.35
1.55-1.580.21135020.17569538X-RAY DIFFRACTION99.32
1.58-1.60.21435010.17949519X-RAY DIFFRACTION99.36
1.6-1.630.21525040.1869577X-RAY DIFFRACTION99.35
1.63-1.660.22025010.19449520X-RAY DIFFRACTION99.41
1.66-1.690.20325010.17649525X-RAY DIFFRACTION99.37
1.69-1.730.19265010.16419510X-RAY DIFFRACTION99.47
1.73-1.760.1835010.15929513X-RAY DIFFRACTION99.16
1.76-1.80.18435000.15969513X-RAY DIFFRACTION99.31
1.8-1.850.18835040.16059560X-RAY DIFFRACTION99.24
1.85-1.90.18155010.16259534X-RAY DIFFRACTION99.23
1.9-1.960.19555020.15979537X-RAY DIFFRACTION99.37
1.96-2.020.18675000.16129487X-RAY DIFFRACTION99.07
2.02-2.090.19434980.16589476X-RAY DIFFRACTION98.62
2.09-2.170.18265000.16379500X-RAY DIFFRACTION98.9
2.17-2.270.18785010.1689515X-RAY DIFFRACTION99.08
2.27-2.390.19525000.16929499X-RAY DIFFRACTION98.97
2.39-2.540.18265030.17559548X-RAY DIFFRACTION99.28
2.54-2.740.18535030.17959568X-RAY DIFFRACTION99.31
2.74-3.020.18645030.17859546X-RAY DIFFRACTION99.21
3.02-3.450.20155020.17359550X-RAY DIFFRACTION98.96
3.45-4.350.18085000.16039492X-RAY DIFFRACTION98.4
4.35-39.860.19625000.17129496X-RAY DIFFRACTION97.31

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