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- PDB-7o8b: Structure of haloalkane dehalogenase variant DhaA80 from Rhodococ... -

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Basic information

Entry
Database: PDB / ID: 7o8b
TitleStructure of haloalkane dehalogenase variant DhaA80 from Rhodococcus rhodochrous
ComponentsHaloalkane dehalogenase
KeywordsHYDROLASE / alpha/beta hydrolase fold
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
methyl sulfate / Haloalkane dehalogenase
Similarity search - Component
Biological speciesRhodococcus rhodochrous (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 15, 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 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

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Assembly

Deposited unit
A: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2022
Polymers33,0901
Non-polymers1121
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.889, 69.551, 83.916
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Haloalkane dehalogenase


Mass: 33089.832 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-V5B / methyl sulfate


Mass: 112.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH4O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2.18 Å3/Da / Density % sol: 43.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M BisTris propane, 0.2M Sodium Fluoride,20% PEG3350, 50% w/v 1-Butyl-3-methylimidazolium methyl sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.75→32.15 Å / Num. obs: 29090 / % possible obs: 99.17 % / Redundancy: 2 % / CC1/2: 0.989 / Net I/σ(I): 1.86
Reflection shellResolution: 1.75→1.792 Å / Num. unique obs: 20 / Rrim(I) all: 0.369

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F60

4f60


Resolution: 1.75→32.15 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.953 / SU B: 7.281 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2244 1532 5 %RANDOM
Rwork0.20827 ---
obs0.20908 29090 99.17 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.616 Å2
Baniso -1Baniso -2Baniso -3
1--3.37 Å2-0 Å20 Å2
2--2.36 Å2-0 Å2
3---1.01 Å2
Refinement stepCycle: LAST / Resolution: 1.75→32.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2343 0 6 133 2482
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0172450
X-RAY DIFFRACTIONr_bond_other_d0.0010.0192264
X-RAY DIFFRACTIONr_angle_refined_deg1.0711.8523356
X-RAY DIFFRACTIONr_angle_other_deg0.9742.6285230
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0875293
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.29421.704135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.9415371
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3051517
X-RAY DIFFRACTIONr_chiral_restr0.0670.2352
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022758
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02564
X-RAY DIFFRACTIONr_mcbond_it0.6980.9441169
X-RAY DIFFRACTIONr_mcbond_other0.6930.9421168
X-RAY DIFFRACTIONr_mcangle_it1.1681.4121463
X-RAY DIFFRACTIONr_mcangle_other1.1681.4141464
X-RAY DIFFRACTIONr_scbond_it0.9371.0261281
X-RAY DIFFRACTIONr_scbond_other0.8131.0171276
X-RAY DIFFRACTIONr_scangle_other1.3031.4951886
X-RAY DIFFRACTIONr_long_range_B_refined4.97711.7182766
X-RAY DIFFRACTIONr_long_range_B_other4.94511.5312755
LS refinement shellResolution: 1.75→1.792 Å
RfactorNum. reflection% reflection
Rfree0.376 106 -
Rwork0.369 2013 -
obs--94.64 %
Refinement TLS params.Method: refined / Origin x: -10.156 Å / Origin y: 13.057 Å / Origin z: -17.473 Å
111213212223313233
T0.3106 Å20.0066 Å2-0.0374 Å2-0.0115 Å2-0.0088 Å2--0.0635 Å2
L1.8292 °20.2824 °2-0.0915 °2-2.3554 °20.1094 °2--1.3163 °2
S0.0154 Å °0.0993 Å °-0.0288 Å °-0.1625 Å °-0.0282 Å °0.1799 Å °0.0014 Å °-0.0882 Å °0.0129 Å °

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