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- PDB-8oe6: Structure of hyperstable haloalkane dehalogenase variant DhaA231 -

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Basic information

Entry
Database: PDB / ID: 8oe6
TitleStructure of hyperstable haloalkane dehalogenase variant DhaA231
ComponentsStructure of hyperstable haloalkane dehalogenase variant DhaA231
KeywordsHYDROLASE / Engineered haloalkane dehalogenase
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.31 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

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Assembly

Deposited unit
A: Structure of hyperstable haloalkane dehalogenase variant DhaA231
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0556
Polymers34,9221
Non-polymers1335
Water7,512417
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area420 Å2
ΔGint-27 kcal/mol
Surface area11520 Å2
Unit cell
Length a, b, c (Å)44.431, 67.998, 122.379
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Structure of hyperstable haloalkane dehalogenase variant DhaA231


Mass: 34921.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 417 / 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: 2.65 Å3/Da / Density % sol: 53.53 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: magnesium chloride, Tris, PEG 8000

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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: 1.31→45.48 Å / Num. obs: 90219 / % possible obs: 99.3 % / Redundancy: 11.7 % / CC1/2: 1 / Net I/σ(I): 19.2
Reflection shellResolution: 1.31→1.33 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3962 / CC1/2: 0.454

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.31→45.48 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 16.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1684 4440 4.93 %0
Rwork0.1542 ---
obs0.1549 90120 99.14 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.31→45.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2399 0 5 417 2821
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152525
X-RAY DIFFRACTIONf_angle_d1.3663456
X-RAY DIFFRACTIONf_dihedral_angle_d8.3231528
X-RAY DIFFRACTIONf_chiral_restr0.102352
X-RAY DIFFRACTIONf_plane_restr0.012456
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.31-1.31990.31871450.31872451X-RAY DIFFRACTION88
1.3199-1.33540.28581370.29372687X-RAY DIFFRACTION94
1.3354-1.35170.26291600.27982743X-RAY DIFFRACTION97
1.3517-1.36880.2951480.25992746X-RAY DIFFRACTION98
1.3688-1.38680.27181290.24972881X-RAY DIFFRACTION100
1.3868-1.40580.25271590.22082791X-RAY DIFFRACTION100
1.4058-1.42590.23981430.20452892X-RAY DIFFRACTION100
1.4259-1.44720.22011260.18142849X-RAY DIFFRACTION100
1.4472-1.46980.21340.17862871X-RAY DIFFRACTION100
1.4698-1.49390.18231550.16622826X-RAY DIFFRACTION100
1.4939-1.51970.1861300.15682853X-RAY DIFFRACTION100
1.5197-1.54730.16851620.15052872X-RAY DIFFRACTION100
1.5473-1.57710.13391440.14652865X-RAY DIFFRACTION100
1.5771-1.60930.18761480.13952847X-RAY DIFFRACTION100
1.6093-1.64430.16311680.14042843X-RAY DIFFRACTION100
1.6443-1.68250.15281640.14182834X-RAY DIFFRACTION100
1.6825-1.72460.14951490.14462893X-RAY DIFFRACTION100
1.7246-1.77120.17581300.14582874X-RAY DIFFRACTION100
1.7712-1.82340.15791460.14562855X-RAY DIFFRACTION100
1.8234-1.88220.17421490.14842894X-RAY DIFFRACTION100
1.8822-1.94950.17451560.14442874X-RAY DIFFRACTION100
1.9495-2.02750.16991330.14912893X-RAY DIFFRACTION100
2.0275-2.11980.15521500.14652897X-RAY DIFFRACTION100
2.1198-2.23160.15631370.14712899X-RAY DIFFRACTION100
2.2316-2.37140.17381420.15142898X-RAY DIFFRACTION100
2.3714-2.55450.16261760.15452886X-RAY DIFFRACTION100
2.5545-2.81150.17261600.15432927X-RAY DIFFRACTION100
2.8115-3.21820.14671680.1542929X-RAY DIFFRACTION100
3.2182-4.05420.14811370.1433000X-RAY DIFFRACTION100
4.0542-45.480.17441550.14973110X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 6.2308 Å / Origin y: -5.3269 Å / Origin z: -15.8813 Å
111213212223313233
T0.1423 Å2-0.0041 Å2-0.0094 Å2-0.1433 Å20.0092 Å2--0.1441 Å2
L1.0885 °2-0.1084 °20.1939 °2-1.0571 °2-0.4865 °2--1.2745 °2
S-0.0125 Å °0.0263 Å °0.0994 Å °0.0375 Å °-0.0308 Å °-0.0307 Å °-0.1137 Å °0.0685 Å °0.0362 Å °
Refinement TLS groupSelection details: all

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