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- PDB-6sp8: Structure of hyperstable haloalkane dehalogenase variant DhaA115 ... -

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Basic information

Entry
Database: PDB / ID: 6sp8
TitleStructure of hyperstable haloalkane dehalogenase variant DhaA115 prepared by the 'soak-and-freeze' method under 150 bar of krypton pressure
ComponentsHaloalkane dehalogenase
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
KRYPTON / THIOCYANATE ION / Haloalkane dehalogenase
Similarity search - Component
Biological speciesRhodococcus rhodochrous (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 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 31, 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
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)70,21039
Polymers66,8002
Non-polymers3,41037
Water11,115617
1
A: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,04719
Polymers33,4001
Non-polymers1,64618
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,16420
Polymers33,4001
Non-polymers1,76319
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.978, 82.045, 144.176
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


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

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Non-polymers , 5 types, 654 molecules

#2: Chemical...
ChemComp-KR / KRYPTON


Mass: 83.798 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: Kr / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CNS / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H26N2O6 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 617 / 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: 3.01 Å3/Da / Density % sol: 59.13 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 3350, Bis-tris propane, potassium isothiocyanate

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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: 1.55→49.46 Å / Num. obs: 116195 / % possible obs: 99 % / Redundancy: 13.5 % / Biso Wilson estimate: 18.17 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.019 / Rrim(I) all: 0.068 / Net I/σ(I): 22.1 / Num. measured all: 1563200 / Scaling rejects: 6
Reflection shell

Diffraction-ID: 1 / Resolution: 1.55→1.58 Å

Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
13.50.8855520.9370.2460.91596.6
12.40.0348300.9990.010.03599.4

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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: 6SP5

6sp5


Resolution: 1.55→49.203 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.49
RfactorNum. reflection% reflection
Rfree0.1812 5785 4.99 %
Rwork0.1601 --
obs0.1611 115973 98.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 70.56 Å2 / Biso mean: 21.053 Å2 / Biso min: 9.73 Å2
Refinement stepCycle: final / Resolution: 1.55→49.203 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4738 0 125 622 5485
Biso mean--32.93 33.38 -
Num. residues----582
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065101
X-RAY DIFFRACTIONf_angle_d0.8496969
X-RAY DIFFRACTIONf_chiral_restr0.057713
X-RAY DIFFRACTIONf_plane_restr0.007905
X-RAY DIFFRACTIONf_dihedral_angle_d8.4654114
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.55-1.56760.2791680.254358597
1.5676-1.58610.2771850.2353361598
1.5861-1.60540.23651870.2109359599
1.6054-1.62570.22232040.2033360898
1.6257-1.64710.24421960.1885362899
1.6471-1.66970.20011840.1806364399
1.6697-1.69350.21172020.1741365099
1.6935-1.71880.20431940.1714363899
1.7188-1.74570.20241870.1702365298
1.7457-1.77430.19221780.1593361798
1.7743-1.80490.1921860.1581356197
1.8049-1.83770.18261960.1636361999
1.8377-1.87310.20211870.15833692100
1.8731-1.91130.20551860.1598365799
1.9113-1.95290.20082050.166366699
1.9529-1.99830.20011850.1585367699
1.9983-2.04830.20431840.15793689100
2.0483-2.10360.19231960.1582367099
2.1036-2.16550.19631780.1627358996
2.1655-2.23540.17641770.1587367999
2.2354-2.31530.16232030.15713698100
2.3153-2.4080.16892000.15643726100
2.408-2.51760.18641970.16113704100
2.5176-2.65040.16912110.1673710100
2.6504-2.81640.19962000.1653364298
2.8164-3.03380.19062020.1617372899
3.0338-3.33910.17431950.15733755100
3.3391-3.82210.15632220.14663784100
3.8221-4.81480.14072060.1309375598
4.8148-49.2030.19341840.1703395798

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