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- PDB-4ufp: Laboratory evolved variant R-C1B1D33 of potato epoxide hydrolase StEH1 -

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Basic information

Entry
Database: PDB / ID: 4ufp
TitleLaboratory evolved variant R-C1B1D33 of potato epoxide hydrolase StEH1
ComponentsEPOXIDE HYDROLASE
KeywordsHYDROLASE / EPOXIDE HYDROLYSIS / ALPHA/BETA-HYDROLASE / DIRECTED EVOLUTION / ASYMMETRIC SYNTHESES
Function / homology
Function and homology information


soluble epoxide hydrolase / 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
soluble epoxide hydrolase
Similarity search - Component
Biological speciesSOLANUM TUBEROSUM (potato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsCarlsson, A.J. / Bauer, P. / Nilsson, M. / Dobritzsch, D. / Kamerlin, S.C.L. / 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 17, 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 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EPOXIDE HYDROLASE
B: EPOXIDE HYDROLASE


Theoretical massNumber of molelcules
Total (without water)74,2612
Polymers74,2612
Non-polymers00
Water23413
1
A: EPOXIDE HYDROLASE


Theoretical massNumber of molelcules
Total (without water)37,1311
Polymers37,1311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: EPOXIDE HYDROLASE


Theoretical massNumber of molelcules
Total (without water)37,1311
Polymers37,1311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.743, 97.105, 121.799
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: _ / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: _ / Auth seq-ID: 3 - 321 / Label seq-ID: 3 - 321

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

NCS oper: (Code: given
Matrix: (0.6997, 0.6946, 0.1673), (0.6634, -0.5447, -0.5131), (-0.2652, 0.47, -0.8419)
Vector: -72.81, 111.9, 18.51)

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Components

#1: Protein EPOXIDE HYDROLASE


Mass: 37130.555 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SOLANUM TUBEROSUM (potato) / Strain: LEMHI RUSSET / Plasmid: PGTACSTEH1-5H / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): XL1 BLUE / References: UniProt: Q41415, epoxide hydrolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE IS C-TERMINALLY HIS-TAGGED AND IS MUTATED AT 6 POSITIONS (P84L, W106L, L109Y, V141K, ...THE SEQUENCE IS C-TERMINALLY HIS-TAGGED AND IS MUTATED AT 6 POSITIONS (P84L, W106L, L109Y, V141K, I155V, F189L)

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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: 2.3 Å3/Da / Density % sol: 46.2 % / Description: NONE
Crystal growpH: 9 / Details: 10% (W/V) PEG10K, 0.1 M BICINE PH 9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.976
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.95→75.9 Å / Num. obs: 13146 / % possible obs: 91.9 % / Observed criterion σ(I): 2 / Redundancy: 5.9 % / Biso Wilson estimate: 47 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 10.2
Reflection shellResolution: 2.95→3.13 Å / Redundancy: 6 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 0.4 / % possible all: 93.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CJP

2cjp


Resolution: 2.95→75.9 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.895 / SU B: 18.534 / SU ML: 0.334 / Cross valid method: THROUGHOUT / ESU R Free: 0.47 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23658 672 5.1 %RANDOM
Rwork0.16988 ---
obs0.17322 12450 90.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.566 Å2
Baniso -1Baniso -2Baniso -3
1--1.41 Å20 Å20 Å2
2--5.1 Å20 Å2
3----3.69 Å2
Refinement stepCycle: LAST / Resolution: 2.95→75.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5100 0 0 13 5113
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195256
X-RAY DIFFRACTIONr_bond_other_d0.0040.025014
X-RAY DIFFRACTIONr_angle_refined_deg1.351.9527144
X-RAY DIFFRACTIONr_angle_other_deg0.968311554
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7955636
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.56223.866238
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.24915850
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.061520
X-RAY DIFFRACTIONr_chiral_restr0.0720.2764
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215882
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021226
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_it3.084.9532550
X-RAY DIFFRACTIONr_mcbond_other3.0794.9522549
X-RAY DIFFRACTIONr_mcangle_it4.8827.4283184
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.3865.2852706
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: 19429 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.951→3.027 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 53 -
Rwork0.291 893 -
obs--92.29 %

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