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- PDB-7o3o: Structure of haloalkane dehalogenase mutant DhaA80(T148L, G171Q, ... -

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Basic information

Entry
Database: PDB / ID: 7o3o
TitleStructure of haloalkane dehalogenase mutant DhaA80(T148L, G171Q, A172V, C176F) from Rhodococcus rhodochrous with ionic liquid
ComponentsHaloalkane dehalogenase
KeywordsHYDROLASE / alpha/beta-hydrolase
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
ETHANOLAMINE / Haloalkane dehalogenase
Similarity search - Component
Biological speciesRhodococcus rhodochrous (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsShaposhnikova, A. / Prudnikova, T. / Kuta Smatanova, I.
Funding support Czech Republic, Germany, 7items
OrganizationGrant numberCountry
Grant Agency of the Czech Republic17-24321S Czech Republic
German Federal Ministry for Education and ResearchDAAD-16-09 Germany
European Regional Development FundCZ.02.1.01/0.0/0.0/15_003/0000441 Czech Republic
European Regional Development FundCZ.02.1.01/0.0/0.0/16_019/0000778 Czech Republic
European Regional Development FundLM2015047 Czech Republic
European Regional Development FundLM2018121 Czech Republic
Ministry of Education (MoE, Czech Republic)CZ.02.1.01/0.0/0.0/16_026/0008451 Czech Republic
CitationJournal: Crystals / Year: 2021
Title: Stabilization of Haloalkane Dehalogenase Structure by Interfacial Interaction with Ionic Liquids
Authors: Shaposhnikova, A. / Kuty, M. / Chaloupkova, R. / Damborsky, J. / Kuta Smatanova, I. / Minofar, B. / Prudnikova, T.
History
DepositionApr 2, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 8, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 15, 2021Group: Database references / Category: citation_author
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id
Revision 2.1Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3633
Polymers34,2661
Non-polymers972
Water6,521362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area380 Å2
ΔGint-14 kcal/mol
Surface area11160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.315, 69.954, 83.816
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Haloalkane dehalogenase /


Mass: 34266.082 Da / Num. of mol.: 1 / Mutation: T148L, G171Q, A172V, C176F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus rhodochrous (bacteria) / Gene: dhaA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A3G2, haloalkane dehalogenase
#2: Chemical ChemComp-ETA / ETHANOLAMINE / Ethanolamine


Type: L-peptide COOH carboxy terminus / Mass: 61.083 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H7NO / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 362 / 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: 2.26 Å3/Da / Density % sol: 45.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M BisTris propane pH6.5, 0.2M Sodium Fluoride, 20% PEG3350, 50% w/v 2-Hydroxyethylammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.918 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 29, 2015
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.25→44.38 Å / Num. obs: 82895 / % possible obs: 99.17 % / Redundancy: 3 % / CC1/2: 0.999 / Net I/σ(I): 23.46
Reflection shellResolution: 1.25→1.282 Å / Num. unique obs: 7209 / Rrim(I) all: 0.054

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F60

4f60


Resolution: 1.25→44.38 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.123 / SU ML: 0.022 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.035 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1528 2101 2.5 %RANDOM
Rwork0.1254 ---
obs0.1261 82895 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 277.32 Å2 / Biso mean: 14.311 Å2 / Biso min: 5.39 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.06 Å2-0 Å2
3----0.05 Å2
Refinement stepCycle: final / Resolution: 1.25→44.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2342 0 5 365 2712
Biso mean--19.24 27 -
Num. residues----290
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0122594
X-RAY DIFFRACTIONr_angle_refined_deg2.0721.6333588
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1145333
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.23522.095148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.20415405
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2961518
X-RAY DIFFRACTIONr_chiral_restr0.1230.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.022114
X-RAY DIFFRACTIONr_rigid_bond_restr13.39432594
LS refinement shellResolution: 1.25→1.282 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.188 151 -
Rwork0.139 5952 -
all-6103 -
obs--97.95 %

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