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- PDB-4uhb: Laboratory evolved variant R-C1 of potato epoxide hydrolase StEH1 -

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Basic information

Entry
Database: PDB / ID: 4uhb
TitleLaboratory evolved variant R-C1 of potato epoxide hydrolase StEH1
ComponentsEPOXIDE HYDROLASE
KeywordsHYDROLASE / DIRECTED EVOLUTION
Function / homology
Function and homology information


epoxide hydrolase activity
Similarity search - Function
Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSOLANUM TUBEROSUM (potato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsNilsson, M.T.I. / Carlsson, A.J. / Dobritzsch, D. / Widersten, M.
CitationJournal: Chembiochem / Year: 2016
Title: Laboratory Evolved Enzymes Provide Snapshots of the Development of Enantioconvergence in Enzyme-Catalyzed Epoxide Hydrolysis.
Authors: Janfalk Carlsson, A. / Bauer, P. / Dobritzsch, D. / Nilsson, M. / Kamerlin, S.C. / Widersten, M.
History
DepositionMar 23, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Database references
Revision 1.2Oct 5, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EPOXIDE HYDROLASE
B: EPOXIDE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,29613
Polymers74,3432
Non-polymers95311
Water10,647591
1
A: EPOXIDE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6026
Polymers37,1721
Non-polymers4305
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: EPOXIDE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6947
Polymers37,1721
Non-polymers5236
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.800, 96.330, 121.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 0 / Auth seq-ID: 3 - 320 / Label seq-ID: 3 - 320

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper: (Code: given
Matrix: (0.7088, 0.6543, -0.2637), (0.6881, -0.559, 0.4626), (0.1552, -0.5094, -0.8464)
Vector: -17.5226, 103.5281, 85.043)

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Components

#1: Protein EPOXIDE HYDROLASE / / STEH1


Mass: 37171.562 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SOLANUM TUBEROSUM (potato) / Plasmid: PGTAC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): XL1-BLUE / References: UniProt: Q41415, epoxide hydrolase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 591 / Source method: isolated from a natural source / Formula: H2O

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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: 2.26 Å3/Da / Density % sol: 46 % / Description: NONE
Crystal growDetails: PROTEIN IN 30 MM TRIS-HCL, PH 7.4 MIXED 1:1 WITH 0.1 M HEPES PH 7.5, 20 % PEG 10,000. THEN SOAKED IN25% (V/V) GLYCEROL, 75 MM HEPES, PH7.68, PEG 10,000 22.5 % (W/V)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979736
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979736 Å / Relative weight: 1
ReflectionResolution: 1.8→32.8 Å / Num. obs: 61576 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 6.6
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CJP

2cjp


Resolution: 1.8→32.83 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.932 / SU B: 5.803 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2109 3006 5 %RANDOM
Rwork0.19865 ---
obs0.19926 57139 97.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.172 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20 Å20 Å2
2--0.96 Å20 Å2
3----0.69 Å2
Refinement stepCycle: LAST / Resolution: 1.8→32.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5124 0 62 591 5777
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0195341
X-RAY DIFFRACTIONr_bond_other_d0.0020.025092
X-RAY DIFFRACTIONr_angle_refined_deg1.651.9577245
X-RAY DIFFRACTIONr_angle_other_deg2.427311740
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9855640
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.34923.833240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.94415850
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2471520
X-RAY DIFFRACTIONr_chiral_restr0.1010.2773
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215931
X-RAY DIFFRACTIONr_gen_planes_other0.0140.021241
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7421.0042560
X-RAY DIFFRACTIONr_mcbond_other0.7361.0042559
X-RAY DIFFRACTIONr_mcangle_it1.151.5023197
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.3171.1832781
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 19498 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 222 -
Rwork0.255 4221 -
obs--99.8 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
117.753-5.464-6.7095.2134.494218.45270.2450.44960.56780.2006-0.24081.0162-0.7031-1.4869-0.00420.21310.02420.09290.19040.04340.458521.509385.7954-0.6651
20.6644-0.0626-0.0990.35990.0181.03380.00490.06680.0198-0.0379-0.00720.017-0.0432-0.02690.00220.03770.0007-0.00520.03960.00440.046336.808791.75141.372
32.02821.7742-1.6395.5162-2.63791.96520.0623-0.04890.00750.2381-0.1587-0.2505-0.15760.23050.09650.0575-0.0142-0.02280.11140.00690.057259.463185.302110.6299
40.587-0.0337-0.10520.7213-0.19220.5521-0.0172-0.0446-0.01880.06750.0033-0.0106-0.00390.02110.01380.02990.0041-0.00950.0372-0.00120.02143.580585.652713.0699
54.76011.7046-0.534734.45089.252614.50110.3461-0.2374-0.53450.8602-0.16450.790.8129-0.8419-0.18150.0962-0.0561-0.02130.16630.04580.17892.113779.564653.6471
60.71050.00240.10061.02420.33051.0151-0.0167-0.1043-0.020.05960.03120.06190.1022-0.037-0.01450.04610.00540.00070.05850.00170.046817.38184.701851.016
74.1575-0.28595.18790.662-0.2477.0471-0.10940.50450.137-0.1798-0.1121-0.1717-0.15670.56630.22150.1151-0.01340.04540.1731-0.00860.122833.55297.958435.4923
80.68610.18040.28420.68420.26131.0664-0.03090.03620.0623-0.16470.03640.1312-0.1235-0.1469-0.00550.05120.0062-0.03760.0760.01360.050514.757595.035234.3875
91.6335-0.17360.07071.3542-0.30971.59760.02130.1009-0.1277-0.1169-0.0015-0.11630.13440.0833-0.01980.0440.01770.00160.0336-0.01830.051226.83377.0338.7461
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 7
2X-RAY DIFFRACTION2A8 - 132
3X-RAY DIFFRACTION3A133 - 157
4X-RAY DIFFRACTION4A158 - 322
5X-RAY DIFFRACTION5B2 - 7
6X-RAY DIFFRACTION6B8 - 132
7X-RAY DIFFRACTION7B133 - 151
8X-RAY DIFFRACTION8B152 - 248
9X-RAY DIFFRACTION9B249 - 321

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