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- PDB-6sp5: Structure of hyperstable haloalkane dehalogenase variant DhaA115 -

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Basic information

Entry
Database: PDB / ID: 6sp5
TitleStructure of hyperstable haloalkane dehalogenase variant DhaA115
ComponentsHaloalkane dehalogenase
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
THIOCYANATE ION / Haloalkane dehalogenase
Similarity search - Component
Biological speciesRhodococcus rhodochrous (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsChmelova, K. / Markova, K. / Damborsky, J. / Marek, M.
Funding support Czech Republic, 3items
OrganizationGrant numberCountry
European CommissionMSCA-IF-2017 792772 Czech Republic
Ministry of Education (Czech Republic)LQ1605, CZ.02.1.01/0.0/0.0/16_013/0001761, LM2015051, LM2015047, LM2015055 Czech Republic
European Union20776, 722610, 814418 Czech Republic
CitationJournal: Chem Sci / Year: 2020
Title: Decoding the intricate network of molecular interactions of a hyperstable engineered biocatalyst.
Authors: Markova, K. / Chmelova, K. / Marques, S.M. / Carpentier, P. / Bednar, D. / Damborsky, J. / Marek, M.
History
DepositionAug 30, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,80611
Polymers66,8002
Non-polymers1,0059
Water10,160564
1
A: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8575
Polymers33,4001
Non-polymers4574
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9496
Polymers33,4001
Non-polymers5495
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.188, 68.121, 83.916
Angle α, β, γ (deg.)90.000, 104.820, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Haloalkane dehalogenase /


Mass: 33400.246 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus rhodochrous (bacteria) / Gene: dhaA / Production host: Escherichia coli (E. coli) / References: UniProt: P0A3G2, haloalkane dehalogenase
#2: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / Bis-tris propane


Mass: 282.334 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H26N2O6 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#3: Chemical
ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CNS / Feature type: SUBJECT OF INVESTIGATION
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 564 / 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: 2.9 Å3/Da / Density % sol: 57.63 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: PEG3350, potassium isothiocyanate, Bis-tris propane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.860999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.860999 Å / Relative weight: 1
ReflectionResolution: 1.6→48.074 Å / Num. obs: 99102 / % possible obs: 98.3 % / Redundancy: 6.8 % / Biso Wilson estimate: 17.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.03 / Rrim(I) all: 0.08 / Net I/σ(I): 13.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.6-1.636.50.63248160.8670.2660.68796.9
8.7-48.076.90.0376560.9990.0150.0499.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.6.2data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HZG
Resolution: 1.6→48.074 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.59
RfactorNum. reflection% reflection
Rfree0.1783 4830 4.88 %
Rwork0.1579 --
obs0.1589 99049 98.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 69.79 Å2 / Biso mean: 22.0951 Å2 / Biso min: 10.75 Å2
Refinement stepCycle: final / Resolution: 1.6→48.074 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4738 0 62 567 5367
Biso mean--31.79 32.5 -
Num. residues----582
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065078
X-RAY DIFFRACTIONf_angle_d0.8446955
X-RAY DIFFRACTIONf_chiral_restr0.057719
X-RAY DIFFRACTIONf_plane_restr0.007906
X-RAY DIFFRACTIONf_dihedral_angle_d7.3684105
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6-1.61820.29621470.2729308897
1.6182-1.63720.23031440.2429312298
1.6372-1.65720.23831650.2272306897
1.6572-1.67820.22421590.2145309496
1.6782-1.70030.24521530.2061297795
1.7003-1.72360.22131620.1951315098
1.7236-1.74820.20821640.1876318498
1.7482-1.77430.20981710.1761311499
1.7743-1.8020.1951480.1725316999
1.802-1.83160.20931750.1622312799
1.8316-1.86310.18931660.159315699
1.8631-1.8970.18221830.1538314599
1.897-1.93350.20291620.1521312199
1.9335-1.9730.17431720.1531317199
1.973-2.01590.1831510.1483316799
2.0159-2.06280.19851640.1561313599
2.0628-2.11440.18041590.1483310697
2.1144-2.17150.16631530.1578303395
2.1715-2.23540.19211520.1531315299
2.2354-2.30760.181500.15193219100
2.3076-2.390.16741550.1474318399
2.39-2.48570.17741410.1557320999
2.4857-2.59890.17561750.1584316499
2.5989-2.73590.17261540.1635317999
2.7359-2.90730.18631900.1614314099
2.9073-3.13170.18671690.1643304595
3.1317-3.44680.18171550.154314998
3.4468-3.94530.15211790.146321099
3.9453-4.96990.13551580.1279323399
4.9699-48.0740.17081540.159320996

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