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- PDB-8oxf: Enantioselective synthesis of fluorine-containing building blocks... -

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Basic information

Entry
Database: PDB / ID: 8oxf
TitleEnantioselective synthesis of fluorine-containing building blocks by employing mutant HHDH in a two-phase system
ComponentsHalohydrin dehalogenase
KeywordsHYDROLASE / Halohydrin dehalogenase / enantioselectivity / chiral azido alcohols
Function / homologyEnoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily / Halohydrin dehalogenase
Function and homology information
Biological speciesArthrobacter sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsMajeric Elenkov, M. / Stefanic, Z.
Funding support Croatia, 1items
OrganizationGrant numberCountry
Croatian Science FoundationIP-2018-01-4493 Croatia
CitationJournal: To Be Published
Title: Enantioselective synthesis of fluorine-containing building blocks by employing mutant HHDH in a two-phase system
Authors: Majeric Elenkov, M. / Stefanic, Z.
History
DepositionMay 2, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Halohydrin dehalogenase
B: Halohydrin dehalogenase
C: Halohydrin dehalogenase
D: Halohydrin dehalogenase
E: Halohydrin dehalogenase
F: Halohydrin dehalogenase
G: Halohydrin dehalogenase
H: Halohydrin dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,49816
Polymers210,2148
Non-polymers2848
Water33,9221883
1
A: Halohydrin dehalogenase
B: Halohydrin dehalogenase
C: Halohydrin dehalogenase
D: Halohydrin dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,2498
Polymers105,1074
Non-polymers1424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12470 Å2
ΔGint-121 kcal/mol
Surface area32610 Å2
MethodPISA
2
E: Halohydrin dehalogenase
F: Halohydrin dehalogenase
G: Halohydrin dehalogenase
H: Halohydrin dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,2498
Polymers105,1074
Non-polymers1424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12490 Å2
ΔGint-116 kcal/mol
Surface area32690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.160, 60.060, 137.110
Angle α, β, γ (deg.)81.730, 80.260, 81.720
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Halohydrin dehalogenase


Mass: 26276.787 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter sp. (bacteria) / Gene: hheA / Production host: Escherichia coli (E. coli) / References: UniProt: Q93MS3
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1883 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.28 Å3/Da / Density % sol: 46.08 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 14% PEG4000, 0.1M CaCl2, 0.1M Tris-HCl buffer

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→56.61 Å / Num. obs: 279665 / % possible obs: 61.8 % / Redundancy: 3.232 % / Biso Wilson estimate: 20.66 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.081 / Rrim(I) all: 0.097 / Χ2: 0.817 / Net I/σ(I): 8.82 / Num. measured all: 903993
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.3-1.381.9092.1910.1798157319151410.942.9697
1.38-1.482.6961.2590.554182268851155130.9621.58422.5
1.48-1.62.9251.5770.69259264102316560.9121.94349.4
1.6-1.753.0740.9791.1216685258921542860.5661.1992.1
1.75-1.963.3860.2673.3315579053332460100.9960.32186.3
1.96-2.263.3740.1556.5614467147007428750.9960.18691.2
2.26-2.763.460.09713.1213192239739381270.990.11595.9
2.76-3.913.4980.04327.0210344830659295740.9970.05196.5
3.91-56.613.4630.02739.15708116879164830.9990.03197.7

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Processing

Software
NameVersionClassification
PHENIX1.19refinement
XSCALEdata scaling
PDB_EXTRACT3.28data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→56.61 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 28.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2428 1991 1.2 %
Rwork0.1972 164082 -
obs0.1977 166073 91.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.63 Å2 / Biso mean: 24.0827 Å2 / Biso min: 9.56 Å2
Refinement stepCycle: final / Resolution: 1.77→56.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14840 0 8 1883 16731
Biso mean--24.79 29.9 -
Num. residues----1944
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.77-1.810.34481430.2904121471229095
1.81-1.860.33891460.2736118551200192
1.86-1.910.36571210.35989714983575
1.91-1.980.3989960.3679192928871
1.98-2.050.31371590.2455122101236995
2.05-2.130.36851400.2643115001164089
2.13-2.230.30061490.2098120321218193
2.23-2.340.31991210.2409107021082383
2.34-2.490.26721520.1918125721272497
2.49-2.680.2661530.1947123651251897
2.68-2.950.22381530.1944125611271498
2.95-3.380.22061560.1776125501270698
3.38-4.260.20481480.158120691221794
4.26-56.610.15151540.1393126131276798

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