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- PDB-8oe2: Structure of hyperstable haloalkane dehalogenase variant DhaA223 -

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Basic information

Entry
Database: PDB / ID: 8oe2
TitleStructure of hyperstable haloalkane dehalogenase variant DhaA223
ComponentsHaloalkane dehalogenase
KeywordsHYDROLASE / Engineered 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 / Resolution: 1.51 Å
AuthorsMarek, M.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Czech Science FoundationGA22-09853S Czech Republic
CitationJournal: Acs Catalysis / Year: 2023
Title: Advancing Enzyme's Stability and Catalytic Efficiency through Synergy of Force-Field Calculations, Evolutionary Analysis, and Machine Learning.
Authors: Kunka, A. / Marques, S.M. / Havlasek, M. / Vasina, M. / Velatova, N. / Cengelova, L. / Kovar, D. / Damborsky, J. / Marek, M. / Bednar, D. / Prokop, Z.
History
DepositionMar 10, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release

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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
C: Haloalkane dehalogenase
D: Haloalkane dehalogenase
E: Haloalkane dehalogenase
F: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,55035
Polymers207,8556
Non-polymers2,69529
Water33,3821853
1
A: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4599
Polymers34,6431
Non-polymers8168
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9585
Polymers34,6431
Non-polymers3164
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9625
Polymers34,6431
Non-polymers3204
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1566
Polymers34,6431
Non-polymers5145
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2457
Polymers34,6431
Non-polymers6026
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7703
Polymers34,6431
Non-polymers1282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.350, 143.144, 106.676
Angle α, β, γ (deg.)90.00, 108.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Haloalkane dehalogenase


Mass: 34642.508 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Gene: dhaA / Production host: Escherichia coli (E. coli) / References: UniProt: P0A3G4, haloalkane dehalogenase

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Non-polymers , 6 types, 1882 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1853 / 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: 2.35 Å3/Da / Density % sol: 47.61 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: Ammonium sulphate, Bis-tris, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.999 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 1.51→47.72 Å / Num. obs: 296214 / % possible obs: 98.2 % / Redundancy: 3.5 % / CC1/2: 0.996 / Net I/σ(I): 7.2
Reflection shellResolution: 1.51→1.53 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 14110 / CC1/2: 0.51

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.51→47.72 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1945 14654 4.95 %0
Rwork0.1683 ---
obs0.1696 295797 98.08 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.51→47.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14324 0 160 1853 16337
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01715185
X-RAY DIFFRACTIONf_angle_d1.42720766
X-RAY DIFFRACTIONf_dihedral_angle_d7.30312351
X-RAY DIFFRACTIONf_chiral_restr0.0932130
X-RAY DIFFRACTIONf_plane_restr0.0122700
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.51-1.52310.33544830.31439035X-RAY DIFFRACTION95
1.5231-1.5410.31074650.29029197X-RAY DIFFRACTION97
1.541-1.55980.2914820.26919429X-RAY DIFFRACTION98
1.5598-1.57960.28815150.24749350X-RAY DIFFRACTION99
1.5796-1.60040.26785010.23639449X-RAY DIFFRACTION99
1.6004-1.62230.2525000.22169452X-RAY DIFFRACTION99
1.6223-1.64550.26175640.21829368X-RAY DIFFRACTION99
1.6455-1.670.22934680.21099445X-RAY DIFFRACTION99
1.67-1.69610.22724440.20369455X-RAY DIFFRACTION99
1.6961-1.72390.23645250.20069464X-RAY DIFFRACTION99
1.7239-1.75370.22545060.1929327X-RAY DIFFRACTION99
1.7537-1.78550.23744300.18759510X-RAY DIFFRACTION99
1.7855-1.81990.2184710.17849334X-RAY DIFFRACTION98
1.8199-1.8570.2144880.17669202X-RAY DIFFRACTION96
1.857-1.89740.20424600.16869232X-RAY DIFFRACTION97
1.8974-1.94160.19714890.17229366X-RAY DIFFRACTION98
1.9416-1.99010.18094620.15469467X-RAY DIFFRACTION99
1.9901-2.04390.18975050.15229542X-RAY DIFFRACTION99
2.0439-2.10410.19155180.15419408X-RAY DIFFRACTION99
2.1041-2.1720.17814930.15199459X-RAY DIFFRACTION99
2.172-2.24960.18244470.1549406X-RAY DIFFRACTION98
2.2496-2.33970.18065020.15449342X-RAY DIFFRACTION98
2.3397-2.44620.18865160.15739391X-RAY DIFFRACTION98
2.4462-2.57510.18894930.15539309X-RAY DIFFRACTION98
2.5751-2.73640.17564890.15879222X-RAY DIFFRACTION96
2.7364-2.94770.1944790.15559425X-RAY DIFFRACTION99
2.9477-3.24430.17335030.15769486X-RAY DIFFRACTION99
3.2443-3.71360.17074500.14949398X-RAY DIFFRACTION98
3.7136-4.67810.15194900.13779380X-RAY DIFFRACTION98
4.6781-47.720.18585160.16869293X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 21.1346 Å / Origin y: 23.735 Å / Origin z: -20.4705 Å
111213212223313233
T0.0916 Å20.0008 Å20.0031 Å2-0.0946 Å2-0.0057 Å2--0.1086 Å2
L0.0191 °20.0037 °20.0002 °2-0.0196 °2-0.0062 °2--0.0202 °2
S-0.0041 Å °-0.0068 Å °0.0026 Å °0.0011 Å °0.0015 Å °0.0027 Å °0.0018 Å °0.0023 Å °-0 Å °
Refinement TLS groupSelection details: all

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