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- PDB-3g0i: Complex of Aspergillus niger epoxide hydrolase with valpromide (2... -

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Basic information

Entry
Database: PDB / ID: 3g0i
TitleComplex of Aspergillus niger epoxide hydrolase with valpromide (2-propylpentanamide)
ComponentsEpoxide hydrolase
KeywordsHYDROLASE / Epoxide hydrolase / alpha/beta hydrolase fold / valpromide / 2-propylpentanamide
Function / homology
Function and homology information


epoxide hydrolase / epoxide metabolic process / epoxide hydrolase activity
Similarity search - Function
Epoxide hydrolase, N-terminal / Epoxide hydrolase N terminus / Epoxide hydrolase / Epoxide hydrolase-like / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-PROPYLPENTANAMIDE / Epoxide hydrolase
Similarity search - Component
Biological speciesAspergillus niger (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsZou, J. / Mowbray, S.L.
Citation
Journal: J.Am.Chem.Soc. / Year: 2009
Title: Directed evolution of an enantioselective epoxide hydrolase: uncovering the source of enantioselectivity at each evolutionary stage
Authors: Reetz, M.T. / Bocola, M. / Wang, L.W. / Sanchis, J. / Cronin, A. / Arand, M. / Zou, J. / Archelas, A. / Bottalla, A.L. / Naworyta, A. / Mowbray, S.L.
#1: Journal: Structure / Year: 2000
Title: Structure of Aspergillus niger epoxide hydrolase at 1.8 A resolution: implications for the structure and function of the mammalian microsomal class of epoxide hydrolases
Authors: Zou, J. / Hallberg, B.M. / Bergfors, T. / Oesch, F. / Arand, M. / Mowbray, S.L. / Jones, T.A.
History
DepositionJan 28, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 9, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Epoxide hydrolase
B: Epoxide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,5354
Polymers88,2482
Non-polymers2862
Water8,179454
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5620 Å2
ΔGint-16 kcal/mol
Surface area28310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.985, 89.655, 75.812
Angle α, β, γ (deg.)90.000, 105.310, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Epoxide hydrolase


Mass: 44124.180 Da / Num. of mol.: 2 / Fragment: UNP residues 5-396
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus niger (mold) / Strain: LCP521 / Gene: hyl1 / Plasmid: PGEF-ANEH336 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9UR30, microsomal epoxide hydrolase
#2: Chemical ChemComp-VPR / 2-PROPYLPENTANAMIDE / VALPROMIDE


Mass: 143.227 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H17NO
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 454 / 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: 2.34 Å3/Da / Density % sol: 47.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20% PEG6000, 0.1M MES, pH6.0, 0.1M unbuffered sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 25, 1999
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. obs: 47596 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.066 / Χ2: 0.877 / Net I/σ(I): 16.947
Reflection shellResolution: 2.1→2.14 Å / Rmerge(I) obs: 0.213 / Num. unique all: 2189 / Χ2: 0.993 / % possible all: 92.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QO7

1qo7


Resolution: 2.1→38.21 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.902 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.231 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.218 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1214 2.6 %RANDOM
Rwork0.175 ---
all0.176 47498 --
obs0.176 47296 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 49.58 Å2 / Biso mean: 14.057 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å2-0.03 Å2
2--0.1 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.1→38.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6218 0 20 454 6692
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0226439
X-RAY DIFFRACTIONr_angle_refined_deg1.1891.9678771
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8625788
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.41923.214280
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.657151031
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3751537
X-RAY DIFFRACTIONr_chiral_restr0.080.2940
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024979
X-RAY DIFFRACTIONr_nbd_refined0.1870.23144
X-RAY DIFFRACTIONr_nbtor_refined0.3070.24431
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2517
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1580.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1280.212
X-RAY DIFFRACTIONr_mcbond_it0.5631.54041
X-RAY DIFFRACTIONr_mcangle_it0.93126379
X-RAY DIFFRACTIONr_scbond_it1.44132767
X-RAY DIFFRACTIONr_scangle_it2.2834.52392
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 78 -
Rwork0.182 3226 -
all-3304 -
obs--94.94 %

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