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- PDB-4b9e: Structure of a putative epoxide hydrolase from Pseudomonas aerugi... -

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Basic information

Entry
Database: PDB / ID: 4b9e
TitleStructure of a putative epoxide hydrolase from Pseudomonas aeruginosa, with bound MFA.
ComponentsPROBABLE EPOXIDE HYDROLASE
KeywordsHYDROLASE / MONOFLUOROACETATE / DEFLUORINASE
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
fluoroacetic acid / Probable epoxide hydrolase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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 4, 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_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_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: PROBABLE EPOXIDE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,61112
Polymers33,6161
Non-polymers99511
Water7,512417
1
A: PROBABLE EPOXIDE HYDROLASE
hetero molecules

A: PROBABLE EPOXIDE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,22124
Polymers67,2322
Non-polymers1,98922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area4770 Å2
ΔGint-133 kcal/mol
Surface area23230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.920, 83.920, 140.950
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-2238-

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-FAH / fluoroacetic acid


Mass: 78.042 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3FO2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 417 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCLONING AND CLEAVAGE OF THE HIS TAG LEFT 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: BEING A SOAK EXPERIMENT, THIS DATA WAS ACTUALLY REFINED AGAINST THE NATIVE UNLIGANDED STRUCTURE WITH PDB CODE 4B9A.
Crystal growpH: 8.5
Details: 0.1 M LI2SO4, 1.25 M (NH4)2SO4, 0.1 M TRIS HCL PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.0064
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0064 Å / Relative weight: 1
ReflectionResolution: 1.4→36.83 Å / Num. obs: 99408 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 6.2 % / Biso Wilson estimate: 13.7 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.5
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 5 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.4 / % possible all: 99.3

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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: 1.4→36.27 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.979 / SU B: 1.143 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.032 / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.13525 4952 5 %RANDOM
Rwork0.1104 ---
obs0.11165 94130 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.522 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2--0.04 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.4→36.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2346 0 57 417 2820
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192540
X-RAY DIFFRACTIONr_bond_other_d0.0020.022395
X-RAY DIFFRACTIONr_angle_refined_deg1.721.973472
X-RAY DIFFRACTIONr_angle_other_deg0.91235469
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3345320
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.30622.031128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.13615388
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1551530
X-RAY DIFFRACTIONr_chiral_restr0.1130.2371
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212909
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02633
X-RAY DIFFRACTIONr_nbd_refined0.2790.21006
X-RAY DIFFRACTIONr_nbd_other0.2210.22006
X-RAY DIFFRACTIONr_nbtor_refined0.1890.21158
X-RAY DIFFRACTIONr_nbtor_other0.1070.21187
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.268
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0910.24
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3110.264
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1790.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it10.9371.5292540
X-RAY DIFFRACTIONr_mcbond_other11.3041.5952394
X-RAY DIFFRACTIONr_mcangle_it
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_restr3.6934934
X-RAY DIFFRACTIONr_sphericity_free40.614588
X-RAY DIFFRACTIONr_sphericity_bonded12.52255198
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 352 -
Rwork0.243 6771 -
obs--98.75 %

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