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- PDB-4b9a: Structure of a putative epoxide hydrolase from Pseudomonas aeruginosa. -

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Basic information

Entry
Database: PDB / ID: 4b9a
TitleStructure of a putative epoxide hydrolase from Pseudomonas aeruginosa.
ComponentsPROBABLE EPOXIDE HYDROLASE
KeywordsHYDROLASE
Function / homology
Function and homology information


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
Probable epoxide hydrolase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsSchmidberger, J.W. / Schnell, R. / Schneider, G.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2013
Title: The Aeropath Project Targeting Pseudomonas Aeruginosa: Crystallographic Studies for Assessment of Potential Targets in Early-Stage Drug Discovery.
Authors: Moynie, L. / Schnell, R. / Mcmahon, S.A. / Sandalova, T. / Boulkerou, W.A. / Schmidberger, J.W. / Alphey, M. / Cukier, C. / Duthie, F. / Kopec, J. / Liu, H. / Jacewicz, A. / Hunter, W.N. / ...Authors: Moynie, L. / Schnell, R. / Mcmahon, S.A. / Sandalova, T. / Boulkerou, W.A. / Schmidberger, J.W. / Alphey, M. / Cukier, C. / Duthie, F. / Kopec, J. / Liu, H. / Jacewicz, A. / Hunter, W.N. / Naismith, J.H. / Schneider, G.
History
DepositionSep 3, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 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_conn / 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_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Oct 1, 2025Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_validate_close_contact / struct_conn
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROBABLE EPOXIDE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,13717
Polymers33,6161
Non-polymers1,52116
Water7,855436
1
A: PROBABLE EPOXIDE HYDROLASE
hetero molecules

A: PROBABLE EPOXIDE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,27434
Polymers67,2322
Non-polymers3,04232
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area8110 Å2
ΔGint-341.2 kcal/mol
Surface area23400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.910, 83.910, 140.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-2250-

HOH

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Components

#1: Protein PROBABLE EPOXIDE HYDROLASE / PA2086


Mass: 33615.980 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA PAO1 (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9I229
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 436 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN
Sequence detailsCLONING AND CUTTING OF THE HIS TAG LEAVES AND EXTRA N- TERMINAL SERINE.

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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: 3.67 Å3/Da / Density % sol: 66.5 % / Description: NONE
Crystal growpH: 8.5
Details: 0.1 M LISO4, 1.25 M (NH4)2SO4, 0.1M TRIS HCL, PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.95373
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 17, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 1.45→72.08 Å / Num. obs: 89489 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 7.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 14
Reflection shellResolution: 1.45→1.53 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.3 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Y37

1y37


Resolution: 1.45→27.45 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.978 / SU B: 1.391 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.037 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 75 AND 76 ARE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.13771 4482 5 %RANDOM
Rwork0.11059 ---
obs0.11199 84909 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: 15.725 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20 Å2
2--0.08 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.45→27.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2353 0 84 436 2873
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0192586
X-RAY DIFFRACTIONr_bond_other_d0.0010.022410
X-RAY DIFFRACTIONr_angle_refined_deg1.7581.9813542
X-RAY DIFFRACTIONr_angle_other_deg0.88535512
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3245323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.15322.093129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.78415388
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0471530
X-RAY DIFFRACTIONr_chiral_restr0.1150.2383
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212938
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02640
X-RAY DIFFRACTIONr_nbd_refined0.290.21072
X-RAY DIFFRACTIONr_nbd_other0.2180.22081
X-RAY DIFFRACTIONr_nbtor_refined0.1890.21177
X-RAY DIFFRACTIONr_nbtor_other0.1070.21216
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2040.278
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.3970.22
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3740.281
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2580.277
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1270.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it12.3861.3442586
X-RAY DIFFRACTIONr_mcbond_other11.7271.42409
X-RAY DIFFRACTIONr_mcangle_it15.5871.9833532
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
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_restr3.84134995
X-RAY DIFFRACTIONr_sphericity_free51.2795104
X-RAY DIFFRACTIONr_sphericity_bonded13.64555267
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 317 -
Rwork0.246 6126 -
obs--99.64 %

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