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- PDB-6zvw: X-RAY STRUCTURE OF THE HALOALKANE DEHALOGENASE HALOTAG7-Q165H LAB... -

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Basic information

Entry
Database: PDB / ID: 6zvw
TitleX-RAY STRUCTURE OF THE HALOALKANE DEHALOGENASE HALOTAG7-Q165H 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 / DI(HYDROXYETHYL)ETHER / Haloalkane dehalogenase
Similarity search - Component
Biological speciesRhodococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsTarnawski, M. / Frei, M. / Hiblot, J. / Johnsson, K.
CitationJournal: To Be Published
Title: X-RAY STRUCTURE OF THE HALOALKANE DEHALOGENASE HALOTAG7-Q165H LABELED WITH A CHLOROALKANE-TETRAMETHYLRHODAMINE FLUOROPHORE SUBSTRATE
Authors: Tarnawski, M. / Frei, M. / Hiblot, J. / Johnsson, K.
History
DepositionJul 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0158
Polymers66,4722
Non-polymers1,5436
Water7,981443
1
A: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9093
Polymers33,2361
Non-polymers6732
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1075
Polymers33,2361
Non-polymers8714
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.180, 47.560, 78.250
Angle α, β, γ (deg.)97.373, 89.971, 114.256
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Haloalkane dehalogenase /


Mass: 33236.000 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

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Non-polymers , 5 types, 449 molecules

#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 / Chloride


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 / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 443 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.23 Å3/Da / Density % sol: 44.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MES pH 6.0, 1.0 M lithium chloride, 20% (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: 1.00006 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00006 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 67810 / % possible obs: 89.3 % / Redundancy: 1.79 % / Biso Wilson estimate: 16.92 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.082 / Net I/σ(I): 5.04
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 1.78 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 1.65 / Num. unique obs: 11604 / CC1/2: 0.755 / % possible all: 91.5

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Y7A

6y7a


Resolution: 1.6→40.21 Å / SU ML: 0.2394 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 34.4432
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2656 3391 5 %
Rwork0.222 64416 -
obs0.2242 67807 89.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.49 Å2
Refinement stepCycle: LAST / Resolution: 1.6→40.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4702 0 103 443 5248
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00764967
X-RAY DIFFRACTIONf_angle_d0.94066788
X-RAY DIFFRACTIONf_chiral_restr0.0597706
X-RAY DIFFRACTIONf_plane_restr0.0078952
X-RAY DIFFRACTIONf_dihedral_angle_d16.55932940
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.43971440.38912734X-RAY DIFFRACTION90.79
1.62-1.650.3911450.36842761X-RAY DIFFRACTION91.85
1.65-1.670.37521440.33982736X-RAY DIFFRACTION91.66
1.67-1.70.3561480.34082813X-RAY DIFFRACTION91.73
1.7-1.730.371420.3122688X-RAY DIFFRACTION90.88
1.73-1.760.34971460.30272774X-RAY DIFFRACTION91.71
1.76-1.790.33641430.28532727X-RAY DIFFRACTION91.84
1.79-1.830.36211450.28272756X-RAY DIFFRACTION89.84
1.83-1.870.34831390.26662625X-RAY DIFFRACTION89.22
1.87-1.910.3791430.2512727X-RAY DIFFRACTION89.55
1.91-1.960.27471400.2342657X-RAY DIFFRACTION90.28
1.96-2.020.3191440.23282730X-RAY DIFFRACTION89.42
2.02-2.080.28491400.23542664X-RAY DIFFRACTION88.12
2.08-2.140.29051370.23152610X-RAY DIFFRACTION87.82
2.14-2.220.27981350.22942563X-RAY DIFFRACTION86.39
2.22-2.310.26991380.2192628X-RAY DIFFRACTION86.06
2.31-2.410.26341380.22422617X-RAY DIFFRACTION87.99
2.41-2.540.27221380.22442626X-RAY DIFFRACTION87.52
2.54-2.70.25871380.21482613X-RAY DIFFRACTION86.81
2.7-2.910.26371410.22442672X-RAY DIFFRACTION88.21
2.91-3.20.24011340.20572563X-RAY DIFFRACTION85.51
3.2-3.660.23981390.19832636X-RAY DIFFRACTION87.82
3.66-4.610.20561400.16232660X-RAY DIFFRACTION88.83
4.61-40.210.18371500.172836X-RAY DIFFRACTION94.31

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