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- PDB-2cjp: Structure of potato (Solanum tuberosum) epoxide hydrolase I (StEH1) -

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Basic information

Entry
Database: PDB / ID: 2cjp
TitleStructure of potato (Solanum tuberosum) epoxide hydrolase I (StEH1)
ComponentsEPOXIDE HYDROLASE
KeywordsHYDROLASE
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
2-PROPYLPENTANAMIDE / soluble epoxide hydrolase
Similarity search - Component
Biological speciesSOLANUM TUBEROSUM (potato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsMowbray, S.L. / Elfstrom, L.T. / Ahlgren, K.M. / Andersson, C.E. / Widersten, M.
CitationJournal: Protein Sci. / Year: 2006
Title: X-Ray Structure of Potato Epoxide Hydrolase Sheds Light on Substrate Specificity in Plant Enzymes.
Authors: Mowbray, S.L. / Elfstrom, L.T. / Ahlgren, K.M. / Andersson, C.E. / Widersten, M.
History
DepositionApr 5, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 15, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval ..._exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.4Dec 13, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)74,7115
Polymers74,3112
Non-polymers4003
Water7,296405
1
A: EPOXIDE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3502
Polymers37,1561
Non-polymers1941
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: EPOXIDE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3613
Polymers37,1561
Non-polymers2052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)55.926, 98.532, 122.033
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.7035, 0.6653, -0.2501), (0.691, -0.5578, 0.4598), (0.1664, -0.4963, -0.8521)
Vector: -19.8967, 106.9727, 85.4732)

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Components

#1: Protein EPOXIDE HYDROLASE


Mass: 37155.551 Da / Num. of mol.: 2
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-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-VPR / 2-PROPYLPENTANAMIDE / VALPROMIDE


Mass: 143.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 405 / 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: 2.2 Å3/Da / Density % sol: 45 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 7.5
Details: 1 UL DROPS OF PROTEIN SOLUTION (7.2 MG/ML, I.E. 0.2 MM, IN 30 MM TRIS-HCL, PH 7.4, 5 MM VALPROMIDE) WERE MIXED WITH 1 UL DROPS OF RESERVOIR SOLUTION (CONTAINING 90 MM NA-HEPES, PH 7.5, 25% ...Details: 1 UL DROPS OF PROTEIN SOLUTION (7.2 MG/ML, I.E. 0.2 MM, IN 30 MM TRIS-HCL, PH 7.4, 5 MM VALPROMIDE) WERE MIXED WITH 1 UL DROPS OF RESERVOIR SOLUTION (CONTAINING 90 MM NA-HEPES, PH 7.5, 25% PEG 10, 000), AND EQUILIBRATED BY SITTING-DROP VAPOR DIFFUSION AT ROOM TEMPERATURE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 3, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.95→31.6 Å / Num. obs: 49514 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 30.41 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 20.9
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 5 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3.1 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VJ5

1vj5


Resolution: 1.95→31.6 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.577 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.19 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUE 1 OF THE A CHAIN, AND 2-3 OF THE B CHAIN WERE OMITTED BECAUSE OF DISORDER. THE PROTEIN WAS EXPRESSED WITH AN ADDITIONAL SEQUENCE AT ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUE 1 OF THE A CHAIN, AND 2-3 OF THE B CHAIN WERE OMITTED BECAUSE OF DISORDER. THE PROTEIN WAS EXPRESSED WITH AN ADDITIONAL SEQUENCE AT THE C-TERMINUS, TSHHHHH, WHICH WAS ALSO NOT VISIBLE IN THE ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.24 2510 5.1 %RANDOM
Rwork0.203 ---
obs0.205 47002 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.8 Å2
Baniso -1Baniso -2Baniso -3
1--1.26 Å20 Å20 Å2
2--2.73 Å20 Å2
3----1.47 Å2
Refinement stepCycle: LAST / Resolution: 1.95→31.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5115 0 27 405 5547
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0225301
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0641.9537202
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2485637
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.02523.833240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.82215844
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7441520
X-RAY DIFFRACTIONr_chiral_restr0.0750.2764
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024068
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1790.22384
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.23529
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1040.2378
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1440.237
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1360.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4751.53276
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.82325142
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.95732340
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.5124.52060
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
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.299 178
Rwork0.286 3369

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