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- PDB-4ufo: Laboratory evolved variant R-C1B1D33E6 of potato epoxide hydrolas... -

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Basic information

Entry
Database: PDB / ID: 4ufo
TitleLaboratory evolved variant R-C1B1D33E6 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: 2.02 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)74,1492
Polymers74,1492
Non-polymers00
Water6,305350
1
A: EPOXIDE HYDROLASE


Theoretical massNumber of molelcules
Total (without water)37,0741
Polymers37,0741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: EPOXIDE HYDROLASE


Theoretical massNumber of molelcules
Total (without water)37,0741
Polymers37,0741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)55.678, 98.444, 122.571
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: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 2 - 320 / Label seq-ID: 2 - 320

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

NCS oper: (Code: given
Matrix: (0.7067, 0.6889, 0.1613), (0.6625, -0.5643, -0.4926), (-0.2483, 0.455, -0.8552)
Vector: -73.96, 116.2, 18.99)

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Components

#1: Protein EPOXIDE HYDROLASE


Mass: 37074.449 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.: 350 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE IS C-TERMINALLY HIS-TAGGED AND IS MUTATED AT 7 POSITIONS (P84L, W106L, L109Y, V141K, ...THE SEQUENCE IS C-TERMINALLY HIS-TAGGED AND IS MUTATED AT 7 POSITIONS (P84L, W106L, L109Y, V141K, I155V, F189L, L266G)

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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: 8.5 / Details: 24% (W/V) PEG5K-MME, 0.1 M TRIS PH 8.5

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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: 2.02→76.75 Å / Num. obs: 45055 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Biso Wilson estimate: 34.1 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.1
Reflection shellResolution: 2.02→2.07 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 2 / % 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: 2.02→76.75 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.933 / SU B: 5.134 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.199 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23182 2208 4.9 %RANDOM
Rwork0.18907 ---
obs0.19115 42775 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.572 Å2
Baniso -1Baniso -2Baniso -3
1--0.69 Å20 Å20 Å2
2--1.96 Å20 Å2
3----1.27 Å2
Refinement stepCycle: LAST / Resolution: 2.02→76.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5117 0 0 350 5467
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0195277
X-RAY DIFFRACTIONr_bond_other_d0.0050.025033
X-RAY DIFFRACTIONr_angle_refined_deg1.3891.9537173
X-RAY DIFFRACTIONr_angle_other_deg1.055311603
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1945641
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.09723.866238
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.66315856
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.571520
X-RAY DIFFRACTIONr_chiral_restr0.0770.2765
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215918
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021230
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_it2.2013.5512564
X-RAY DIFFRACTIONr_mcbond_other2.1993.5512563
X-RAY DIFFRACTIONr_mcangle_it3.0985.3153202
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.683.8252713
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: 19327 / 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: 2.02→2.072 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 153 -
Rwork0.291 3131 -
obs--100 %

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