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- PDB-4o08: Crystal structure of bacillus megaterium epoxide hydrolase in com... -

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Basic information

Entry
Database: PDB / ID: 4o08
TitleCrystal structure of bacillus megaterium epoxide hydrolase in complex with an inhibitor
ComponentsSoluble epoxide hydrolase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / A/B HYDROLASE FOLD / EPOXIDE HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


pyrimidine-5'-nucleotide nucleosidase activity / pyrimidine-5'-nucleotide nucleosidase
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-phenoxyacetamide / Soluble epoxide hydrolase
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.95 Å
AuthorsKong, X.D. / Zhou, J.H. / Xu, J.H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Engineering of an epoxide hydrolase for efficient bioresolution of bulky pharmaco substrates.
Authors: Kong, X.D. / Yuan, S. / Li, L. / Chen, S. / Xu, J.H. / Zhou, J.
History
DepositionDec 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 19, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: Soluble epoxide hydrolase
B: Soluble epoxide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,39510
Polymers74,3512
Non-polymers1,0448
Water8,737485
1
A: Soluble epoxide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8216
Polymers37,1761
Non-polymers6465
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Soluble epoxide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5744
Polymers37,1761
Non-polymers3983
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)108.541, 108.541, 116.843
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsBIOMOLECULE: 1, 2 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA. COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. BIOMOLECULE: 1 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC SOFTWARE USED: PISA APPLY THE FOLLOWING TO CHAINS: A BIOMT1 1 1.000000 0.000000 0.000000 0.00000 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 BIOMOLECULE: 2 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC SOFTWARE USED: PISA APPLY THE FOLLOWING TO CHAINS: B BIOMT1 1 1.000000 0.000000 0.000000 0.00000 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 BIOMT3 1 0.000000 0.000000 1.000000 0.00000

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Components

#1: Protein Soluble epoxide hydrolase


Mass: 37175.746 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus megaterium (bacteria) / Strain: ECU1001 / Plasmid: PET 28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: G9BEX6, pyrimidine-5'-nucleotide nucleosidase
#2: Chemical
ChemComp-PO6 / 2-phenoxyacetamide


Mass: 151.163 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H9NO2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 485 / 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: 2.31 Å3/Da / Density % sol: 46.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M LI2SO4, 0.1M TRIS-HCL, 2.0M (NH4) 2SO4, PH 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 6, 2011
RadiationMonochromator: VARIMAX-HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→79.523 Å / Num. obs: 51301 / % possible obs: 99.7 % / Observed criterion σ(I): -3
Reflection shellResolution: 1.95→2.02 Å / % possible all: 99.6

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Processing

Software
NameVersionClassification
SHELXSphasing
PHENIX(PHENIX.REFINE: 1.7_637)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.95→44.83 Å / SU ML: 0.25 / σ(F): 0 / Phase error: 19.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.207 2564 5.09 %
Rwork0.17 --
obs0.171 50352 97.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.39 Å2 / ksol: 0.36 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.6238 Å2-0 Å20 Å2
2---1.6238 Å2-0 Å2
3---3.2477 Å2
Refinement stepCycle: LAST / Resolution: 1.95→44.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4725 0 70 485 5280
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074992
X-RAY DIFFRACTIONf_angle_d1.0356772
X-RAY DIFFRACTIONf_dihedral_angle_d13.5981840
X-RAY DIFFRACTIONf_chiral_restr0.073682
X-RAY DIFFRACTIONf_plane_restr0.005893
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.98750.29151600.22712475X-RAY DIFFRACTION94
1.9875-2.02810.25741420.21092546X-RAY DIFFRACTION95
2.0281-2.07220.2431240.18492561X-RAY DIFFRACTION95
2.0722-2.12040.22421210.18212572X-RAY DIFFRACTION96
2.1204-2.17340.24811370.182575X-RAY DIFFRACTION97
2.1734-2.23220.22481530.17022567X-RAY DIFFRACTION97
2.2322-2.29790.21861380.17942628X-RAY DIFFRACTION98
2.2979-2.3720.23821300.17682660X-RAY DIFFRACTION98
2.372-2.45680.23451580.17382637X-RAY DIFFRACTION99
2.4568-2.55510.20761400.16742668X-RAY DIFFRACTION99
2.5551-2.67140.24341310.1712672X-RAY DIFFRACTION99
2.6714-2.81220.22641480.18192686X-RAY DIFFRACTION99
2.8122-2.98840.23481140.20052724X-RAY DIFFRACTION99
2.9884-3.21910.25961430.19672715X-RAY DIFFRACTION100
3.2191-3.54290.19741470.16952722X-RAY DIFFRACTION99
3.5429-4.05530.17131900.14282689X-RAY DIFFRACTION99
4.0553-5.10810.15341290.12692786X-RAY DIFFRACTION99
5.1081-44.83840.18681590.17832905X-RAY DIFFRACTION99

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