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- PDB-4ufn: Laboratory evolved variant R-C1B1 of potato epoxide hydrolase StEH1 -

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Basic information

Entry
Database: PDB / ID: 4ufn
TitleLaboratory evolved variant R-C1B1 of potato epoxide hydrolase StEH1
ComponentsEPOXIDE HYDROLASE
KeywordsHYDROLASE / EPOXIDE HYDROLYSIS / ALPHA/BETA-HYDROLASE / DIRECTED EVOLUTION / ASYMMETRIC SYNTHESES
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
1,4-DIETHYLENE DIOXIDE / Epoxide hydrolase
Similarity search - Component
Biological speciesSOLANUM TUBEROSUM (potato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCarlsson, A.J. / Bauer, P. / Nilsson, M. / Dobritzsch, D. / Kamerlin, S.C.L. / Widersten, M.
CitationJournal: Org.Biomol.Chem. / Year: 2016
Title: Conformational Diversity and Enantioconvergence in Potato Epoxide Hydrolase 1.
Authors: Bauer, P. / Carlsson, A.J. / Amrein, B.A. / Dobritzsch, D. / Widersten, M. / Kamerlin, S.C.L.
History
DepositionMar 17, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 1.2Dec 20, 2023Group: 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)74,5054
Polymers74,3292
Non-polymers1762
Water11,566642
1
A: EPOXIDE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2532
Polymers37,1651
Non-polymers881
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: EPOXIDE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2532
Polymers37,1651
Non-polymers881
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)56.003, 99.140, 123.461
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: 2 - 321 / Label seq-ID: 2 - 321

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

NCS oper: (Code: given
Matrix: (0.7045, 0.6925, 0.1555), (0.665, -0.5675, -0.4856), (-0.248, 0.4455, -0.8603)
Vector: -74.64, 117.4, 20.09)

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Components

#1: Protein EPOXIDE HYDROLASE


Mass: 37164.570 Da / Num. of mol.: 2 / Fragment: RESIDUES 3-321 / 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: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 642 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE IS N-TERMINALLY HIS-TAGGED AND IS MUTATED AT 5 POSITIONS (P84L, W106L, L109Y, V141K, I155V)

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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 % / Description: NONE
Crystal growpH: 8
Details: 18% (W/V) PEG5K-MME 0.1 M TRIS PH 8.0 5% (V/V) 1,4-DIOXANE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2→99.14 Å / Num. obs: 47143 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 5.7 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 9
Reflection shellResolution: 2→2.05 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CJP

2cjp


Resolution: 2→77.3 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.132 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.182 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.21111 2292 4.9 %RANDOM
Rwork0.17055 ---
obs0.17255 44563 99.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.371 Å2
Baniso -1Baniso -2Baniso -3
1-1.58 Å20 Å20 Å2
2--0.08 Å20 Å2
3----1.66 Å2
Refinement stepCycle: LAST / Resolution: 2→77.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5126 0 12 642 5780
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0195334
X-RAY DIFFRACTIONr_bond_other_d0.0040.025090
X-RAY DIFFRACTIONr_angle_refined_deg1.3041.9567253
X-RAY DIFFRACTIONr_angle_other_deg1.002311747
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8215650
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.58123.909243
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.30415870
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4781520
X-RAY DIFFRACTIONr_chiral_restr0.0760.2770
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215980
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021244
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_it1.5162.4362570
X-RAY DIFFRACTIONr_mcbond_other1.5152.4362569
X-RAY DIFFRACTIONr_mcangle_it2.3933.6443212
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9482.6322764
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: 19314 / 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→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 147 -
Rwork0.232 3231 -
obs--99.18 %

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