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- PDB-6ty7: Crystal structure of haloalkane dehalogenase variant DhaA115 doma... -

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Basic information

Entry
Database: PDB / ID: 6ty7
TitleCrystal structure of haloalkane dehalogenase variant DhaA115 domain-swapped dimer type-1
ComponentsHaloalkane dehalogenase variant DhaA115 domain-swapped dimer type-1
KeywordsHYDROLASE / Haloalkane dehalogenase
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
NITRATE ION / Haloalkane dehalogenase
Similarity search - Component
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsMarkova, K. / Chaloupkova, R. / 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 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 9, 2022Group: Advisory / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_unobs_or_zero_occ_atoms
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 DhaA115 domain-swapped dimer type-1
B: Haloalkane dehalogenase variant DhaA115 domain-swapped dimer type-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,74911
Polymers68,8952
Non-polymers8549
Water9,782543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16120 Å2
ΔGint-84 kcal/mol
Surface area22020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.930, 75.650, 143.900
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Haloalkane dehalogenase variant DhaA115 domain-swapped dimer type-1


Mass: 34447.383 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A3G2*PLUS, haloalkane dehalogenase

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Non-polymers , 6 types, 552 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#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 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#6: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 543 / 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: 2.26 Å3/Da / Density % sol: 45.45 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG 20000, PEG MME 550, sodium nitrate, disodium hydrogenphosphate, ammonium sulphate, MES, imidazole

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.5→75.65 Å / Num. obs: 96088 / % possible obs: 97.8 % / Redundancy: 5.9 % / Biso Wilson estimate: 11.961 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.082 / Net I/σ(I): 11.8
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 3.4 % / Num. unique obs: 5749 / CC1/2: 0.546 / % possible all: 81.2

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Phasing

PhasingMethod: molecular replacement

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Processing

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

4hzg


Resolution: 1.5→71.95 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1935 4710 4.9 %
Rwork0.1694 91378 -
obs0.1706 96088 97.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 66.72 Å2 / Biso mean: 17.8369 Å2 / Biso min: 7.78 Å2
Refinement stepCycle: final / Resolution: 1.5→71.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4789 0 55 546 5390
Biso mean--30.06 26.81 -
Num. residues----587
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5-1.51710.3021390.271237777
1.5171-1.53490.29651310.2733250482
1.5349-1.55360.29971140.2608266786
1.5536-1.57330.32111350.2477283392
1.5733-1.5940.28761620.2318297296
1.594-1.61580.24211410.2255302699
1.6158-1.63890.23991640.2087305299
1.6389-1.66340.23231480.1948306899
1.6634-1.68940.20571680.18363087100
1.6894-1.71710.20281810.17173070100
1.7171-1.74670.19111410.16253109100
1.7467-1.77840.20061560.1653068100
1.7784-1.81270.19741490.1653132100
1.8127-1.84970.2071820.16743071100
1.8497-1.88990.19521610.16593092100
1.8899-1.93380.18391450.16613127100
1.9338-1.98220.19791720.1653077100
1.9822-2.03580.18381670.16713097100
2.0358-2.09570.17681770.16843121100
2.0957-2.16340.20031630.16793094100
2.1634-2.24070.22061600.16373126100
2.2407-2.33040.18311650.15753109100
2.3304-2.43650.18531570.16833122100
2.4365-2.56490.17831810.16493118100
2.5649-2.72570.2111470.17163131100
2.7257-2.93610.20411600.17353178100
2.9361-3.23160.18721640.17643151100
3.2316-3.69920.18441650.15863173100
3.6992-4.66050.14481450.13883265100
4.6605-71.950.17171700.16263361100

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