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- PDB-6zvv: X-RAY STRUCTURE OF THE HALOALKANE DEHALOGENASE HALOTAG7-P174W LAB... -

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Basic information

Entry
Database: PDB / ID: 6zvv
TitleX-RAY STRUCTURE OF THE HALOALKANE DEHALOGENASE HALOTAG7-P174W 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 / 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. / Frei, M. / Hiblot, J. / Johnsson, K.
CitationJournal: To Be Published
Title: X-RAY STRUCTURE OF THE HALOALKANE DEHALOGENASE HALOTAG7-P174W 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
Revision 1.2Nov 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)136,17515
Polymers133,2604
Non-polymers2,91511
Water24,7351373
1
A: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0804
Polymers33,3151
Non-polymers7653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0284
Polymers33,3151
Non-polymers7133
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9883
Polymers33,3151
Non-polymers6732
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0804
Polymers33,3151
Non-polymers7653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.260, 53.030, 163.210
Angle α, β, γ (deg.)90.000, 93.746, 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

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Haloalkane dehalogenase


Mass: 33315.074 Da / Num. of mol.: 4
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, 1384 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.: 4 / Source method: obtained synthetically / Formula: C35H43ClN3O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / 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: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1373 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.28 Å3/Da / Density % sol: 45.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M calcium acetate, 20% (m/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00003 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 5, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 230075 / % possible obs: 97.4 % / Redundancy: 3.16 % / Biso Wilson estimate: 14.16 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.067 / Net I/σ(I): 10.6
Reflection shellResolution: 1.4→1.5 Å / Redundancy: 2.46 % / Rmerge(I) obs: 0.289 / Mean I/σ(I) obs: 3.18 / Num. unique obs: 40203 / CC1/2: 0.82 / % possible all: 91.6

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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: 1.4→42.29 Å / SU ML: 0.1543 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 22.1738
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2251 11503 5 %
Rwork0.1993 218539 -
obs0.2006 230042 97.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.71 Å2
Refinement stepCycle: LAST / Resolution: 1.4→42.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9401 0 193 1373 10967
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00619949
X-RAY DIFFRACTIONf_angle_d0.883613606
X-RAY DIFFRACTIONf_chiral_restr0.08121413
X-RAY DIFFRACTIONf_plane_restr0.00661904
X-RAY DIFFRACTIONf_dihedral_angle_d8.63024849
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.27163110.24715912X-RAY DIFFRACTION79.46
1.42-1.430.26243360.24156383X-RAY DIFFRACTION85.84
1.43-1.450.27533570.23216783X-RAY DIFFRACTION91.99
1.45-1.470.26363810.22287238X-RAY DIFFRACTION96.54
1.47-1.490.24863850.21127322X-RAY DIFFRACTION99.41
1.49-1.510.24783930.20527454X-RAY DIFFRACTION99.81
1.51-1.530.23753910.19517435X-RAY DIFFRACTION99.73
1.53-1.550.22133900.19627417X-RAY DIFFRACTION99.63
1.55-1.580.24563890.20167380X-RAY DIFFRACTION99.65
1.58-1.60.23953920.19757448X-RAY DIFFRACTION99.56
1.6-1.630.2163910.19627441X-RAY DIFFRACTION99.66
1.63-1.660.24383890.19587383X-RAY DIFFRACTION99.34
1.66-1.690.22793880.19437374X-RAY DIFFRACTION99.44
1.69-1.730.23373910.1947416X-RAY DIFFRACTION99.34
1.73-1.760.22713900.19647422X-RAY DIFFRACTION99.2
1.76-1.80.22563850.19697318X-RAY DIFFRACTION98.81
1.8-1.850.25243890.19977385X-RAY DIFFRACTION98.76
1.85-1.90.22483900.19817409X-RAY DIFFRACTION98.8
1.9-1.960.21313900.19967405X-RAY DIFFRACTION98.96
1.96-2.020.23493850.20257319X-RAY DIFFRACTION98.64
2.02-2.090.2153880.19797366X-RAY DIFFRACTION98.4
2.09-2.170.22093860.20047335X-RAY DIFFRACTION98.61
2.17-2.270.24223880.19837389X-RAY DIFFRACTION98.48
2.27-2.390.22253860.19987338X-RAY DIFFRACTION97.93
2.39-2.540.21793840.19917295X-RAY DIFFRACTION97.03
2.54-2.740.23013880.20867362X-RAY DIFFRACTION98.08
2.74-3.020.22393890.20357391X-RAY DIFFRACTION98.31
3.02-3.450.21133890.19867401X-RAY DIFFRACTION98.04
3.45-4.350.22093930.18987450X-RAY DIFFRACTION97.83
4.35-42.290.20563990.19297568X-RAY DIFFRACTION97.21

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