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- PDB-6xtc: Crystal structure of haloalkane dehalogenase variant DhaA177 doma... -

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Basic information

Entry
Database: PDB / ID: 6xtc
TitleCrystal structure of haloalkane dehalogenase variant DhaA177 domain-swapped dimer type-3
ComponentsHaloalkane dehalogenase variant DhaA177 domain-swapped dimer type-3
KeywordsHYDROLASE / Haloalkane dehalogenase
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
Similarity search - Domain/homology
Haloalkane dehalogenase
Similarity search - Component
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.543 Å
AuthorsMarkova, K. / Damborsky, J. / Marek, M.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
European CommissionMSCA-IF-2017 792772 Czech Republic
CitationJournal: Acs Catalysis / Year: 2021
Title: Computational Enzyme Stabilization Can Affect Folding Energy Landscapes and Lead to Catalytically Enhanced Domain-Swapped Dimers
Authors: Markova, K. / Kunka, A. / Chmelova, K. / Havlasek, M. / Babkova, P. / Marques, S.M. / Vasina, M. / Planas-Iglesias, J. / Chaloupkova, R. / Bednar, D. / Prokop, Z. / Damborsky, J. / Marek, M.
History
DepositionJan 16, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 9, 2022Group: Database references / Category: citation / citation_author / database_2
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.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 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 variant DhaA177 domain-swapped dimer type-3
B: Haloalkane dehalogenase variant DhaA177 domain-swapped dimer type-3
C: Haloalkane dehalogenase variant DhaA177 domain-swapped dimer type-3
D: Haloalkane dehalogenase variant DhaA177 domain-swapped dimer type-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,48741
Polymers136,9404
Non-polymers3,54637
Water4,540252
1
A: Haloalkane dehalogenase variant DhaA177 domain-swapped dimer type-3
B: Haloalkane dehalogenase variant DhaA177 domain-swapped dimer type-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,86427
Polymers68,4702
Non-polymers2,39425
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17140 Å2
ΔGint-351 kcal/mol
Surface area22990 Å2
MethodPISA
2
C: Haloalkane dehalogenase variant DhaA177 domain-swapped dimer type-3
D: Haloalkane dehalogenase variant DhaA177 domain-swapped dimer type-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,62314
Polymers68,4702
Non-polymers1,15312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15820 Å2
ΔGint-257 kcal/mol
Surface area22700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.809, 124.182, 133.885
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 variant DhaA177 domain-swapped dimer type-3


Mass: 34235.070 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A3G2*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 35 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 3.67 Å3/Da / Density % sol: 66.46 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: Ammonium sulphate, lithium sulphate, tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99987 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Aug 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 2.54→45.524 Å / Num. obs: 66790 / % possible obs: 99.8 % / Redundancy: 13.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.163 / Rpim(I) all: 0.046 / Rrim(I) all: 0.169 / Net I/σ(I): 15.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.54-2.613.71.7885876142950.8310.4971.8571.697.1
11.92-45.5211.60.029861374410.0090.03169.498.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.6.2data scaling
PHASERphasing
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HZG

4hzg


Resolution: 2.543→45.524 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.15
RfactorNum. reflection% reflection
Rfree0.2894 3413 5.18 %
Rwork0.2264 --
obs0.2297 65918 98.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 118.83 Å2 / Biso mean: 56.032 Å2 / Biso min: 18.27 Å2
Refinement stepCycle: final / Resolution: 2.543→45.524 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9396 0 187 256 9839
Biso mean--83.75 55.53 -
Num. residues----1164
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.543-2.57890.38911510.3429248996
2.5789-2.61740.41281300.32792591100
2.6174-2.65830.4521420.3162586100
2.6583-2.70190.36691150.30542638100
2.7019-2.74850.41841340.28622623100
2.7485-2.79840.34061260.26852625100
2.7984-2.85220.38771180.25932616100
2.8522-2.91050.32761520.25112589100
2.9105-2.97370.28541440.2492611100
2.9737-3.04290.30821520.25122629100
3.0429-3.1190.35741320.24742599100
3.119-3.20330.29311660.23542605100
3.2033-3.29750.3221590.23582579100
3.2975-3.40390.31231590.24572613100
3.4039-3.52550.29011290.23862667100
3.5255-3.66660.50321040.3504236390
3.6666-3.83340.4471220.3358237189
3.8334-4.03540.23321870.202250597
4.0354-4.28810.19981780.15962601100
4.2881-4.61890.20651680.15172640100
4.6189-5.08310.23391410.15722681100
5.0831-5.81740.24421000.18372725100
5.8174-7.32430.31061460.22012722100
7.3243-45.5240.22021580.19682837100

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