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- PDB-8ags: Cyclohexane epoxide soak of epoxide hydrolase from metagenomic so... -

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Basic information

Entry
Database: PDB / ID: 8ags
TitleCyclohexane epoxide soak of epoxide hydrolase from metagenomic source ch65 resulting in halogenated compound in the active site
ComponentsAlpha/beta epoxide hydrolase
KeywordsHYDROLASE / Alpha/beta hydrolase fold / complex with substrate / limonene epoxide
Function / homologyEpoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / hydrolase activity / 2-CHLOROPHENOL / TRIETHYLENE GLYCOL / Alpha/beta epoxide hydrolase
Function and homology information
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsIsupov, M.N. / De Rose, S.A. / Mitchell, D. / Littlechild, J.A.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Union (EU)265933European Union
CitationJournal: To Be Published
Title: Complexes of epoxide hydrolase from metagenomic source ch65
Authors: Isupov, M.N. / De Rose, S.A. / Mitchell, D. / Littlechild, J.A. / Parker, E. / Ferrandi, E. / Guazzelli, E. / Monti, D.
History
DepositionJul 20, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: Alpha/beta epoxide hydrolase
BBB: Alpha/beta epoxide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,20017
Polymers69,8812
Non-polymers1,31915
Water5,405300
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.210, 46.190, 92.140
Angle α, β, γ (deg.)90.000, 98.000, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21BBB

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 3 - 289 / Label seq-ID: 3 - 289

Dom-IDComponent-IDAuth asym-IDLabel asym-ID
11AAAA
22BBBB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

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Protein , 1 types, 2 molecules AAABBB

#1: Protein Alpha/beta epoxide hydrolase


Mass: 34940.449 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenome (others)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A1U9WZ52

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Non-polymers , 6 types, 315 molecules

#2: Chemical ChemComp-2CH / 2-CHLOROPHENOL


Mass: 128.556 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5ClO / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / 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: 2.09 Å3/Da / Density % sol: 41.06 %
Crystal growTemperature: 291 K / Method: microbatch
Details: Morpheus crystallisation kit C1; 40% v/v PEG 500* MME; 20% w/v PEG 20000, thecrystal was soaked with cyclohexane epoxide substrate at pH 6.5 for 2 hours to produce halogenated product.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.61→46.19 Å / Num. obs: 73190 / % possible obs: 97.5 % / Redundancy: 3.2 % / CC1/2: 0.999 / Net I/σ(I): 12.2
Reflection shellResolution: 1.61→1.64 Å / Num. unique obs: 3660 / CC1/2: 0.43

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
Cootmodel building
BUSTERrefinement
PARROTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ng7

5ng7


Resolution: 1.61→45.663 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.635 / SU ML: 0.087 / Cross valid method: FREE R-VALUE / ESU R: 0.103 / ESU R Free: 0.105 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2226 3603 4.924 %
Rwork0.1803 69572 -
all0.182 --
obs-73175 97.448 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 33.552 Å2
Baniso -1Baniso -2Baniso -3
1--1.032 Å20 Å2-1.534 Å2
2--0.244 Å20 Å2
3---1.173 Å2
Refinement stepCycle: LAST / Resolution: 1.61→45.663 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4839 0 83 300 5222
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0125566
X-RAY DIFFRACTIONr_angle_refined_deg1.7271.6387623
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8045728
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.82822.432292
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.664151066
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.8741531
X-RAY DIFFRACTIONr_chiral_restr0.1180.2711
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024191
X-RAY DIFFRACTIONr_nbd_refined0.230.22593
X-RAY DIFFRACTIONr_nbtor_refined0.320.23691
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2289
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.280.298
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1790.227
X-RAY DIFFRACTIONr_mcbond_it5.8967.8032501
X-RAY DIFFRACTIONr_mcangle_it6.89213.0683163
X-RAY DIFFRACTIONr_scbond_it8.9699.2963065
X-RAY DIFFRACTIONr_scangle_it10.3614.8814383
X-RAY DIFFRACTIONr_lrange_it11.01858.27223665
X-RAY DIFFRACTIONr_ncsr_local_group_10.1160.0510345
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.1160.05008
12BBBX-RAY DIFFRACTIONLocal ncs0.1160.05008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.61-1.6520.3722430.355204X-RAY DIFFRACTION98.4813
1.652-1.6970.3692430.3345004X-RAY DIFFRACTION98.1298
1.697-1.7460.3112420.3024836X-RAY DIFFRACTION97.6351
1.746-1.80.2992600.2624687X-RAY DIFFRACTION97.4202
1.8-1.8590.2772210.2344592X-RAY DIFFRACTION97.706
1.859-1.9240.2462160.2064480X-RAY DIFFRACTION97.6096
1.924-1.9960.2222310.1844232X-RAY DIFFRACTION97.8943
1.996-2.0780.2372430.1894146X-RAY DIFFRACTION98.6292
2.078-2.170.2111990.1843961X-RAY DIFFRACTION98.3917
2.17-2.2760.2311820.1833783X-RAY DIFFRACTION97.8046
2.276-2.3980.2251840.1783641X-RAY DIFFRACTION98.1524
2.398-2.5430.2291910.1753398X-RAY DIFFRACTION97.7396
2.543-2.7180.241960.1723222X-RAY DIFFRACTION98.1902
2.718-2.9350.2411510.1772932X-RAY DIFFRACTION96.6761
2.935-3.2140.2191450.1852701X-RAY DIFFRACTION95.4393
3.214-3.5910.1921350.1622430X-RAY DIFFRACTION95
3.591-4.1430.181110.1392173X-RAY DIFFRACTION94.9688
4.143-5.0640.183980.1311840X-RAY DIFFRACTION95.2802
5.064-7.1180.219720.1831457X-RAY DIFFRACTION95.6223
7.118-45.6630.217400.186853X-RAY DIFFRACTION94.6978

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