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- PDB-3hea: The L29P/L124I mutation of Pseudomonas fluorescens esterase -

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Basic information

Entry
Database: PDB / ID: 3hea
TitleThe L29P/L124I mutation of Pseudomonas fluorescens esterase
ComponentsArylesterase
KeywordsHYDROLASE / alpha/beta hydrolase / esterase / covalent adduct / tetrahedral intermediate / Oxidoreductase / Peroxidase
Function / homology
Function and homology information


arylesterase / Oxidoreductases / arylesterase activity / peroxidase 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
ETHYL ACETATE / Arylesterase
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKazlauskas, R.J. / Schrag, J.D. / Cheeseman, J.D. / Morley, K.L.
Citation
Journal: Biochemistry / Year: 2010
Title: Switching catalysis from hydrolysis to perhydrolysis in Pseudomonas fluorescens esterase.
Authors: Yin de, L.T. / Bernhardt, P. / Morley, K.L. / Jiang, Y. / Cheeseman, J.D. / Purpero, V. / Schrag, J.D. / Kazlauskas, R.J.
#1: Journal: Angew.Chem.Int.Ed.Engl. / Year: 2005
Title: Molecular basis of perhydrolase activity in serine hydrolases.
Authors: Bernhardt, P. / Hult, K. / Kazlauskas, R.J.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Structure of an aryl esterase from Pseudomonas fluorescens.
Authors: Cheeseman, J.D. / Tocilj, A. / Park, S. / Schrag, J.D. / Kazlauskas, R.J.
History
DepositionMay 8, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / 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: Arylesterase
B: Arylesterase
C: Arylesterase
D: Arylesterase
E: Arylesterase
F: Arylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,95150
Polymers179,8676
Non-polymers4,08444
Water19,0421057
1
A: Arylesterase
B: Arylesterase
C: Arylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,07626
Polymers89,9343
Non-polymers2,14223
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9830 Å2
ΔGint-84 kcal/mol
Surface area27760 Å2
MethodPISA
2
D: Arylesterase
E: Arylesterase
F: Arylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,87624
Polymers89,9343
Non-polymers1,94221
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9720 Å2
ΔGint-45 kcal/mol
Surface area27390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.586, 145.586, 128.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

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Components

#1: Protein
Arylesterase / Aryl-ester hydrolase / PFE / Putative bromoperoxidase


Mass: 29977.912 Da / Num. of mol.: 6 / Mutation: L29P/L124I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: P22862, arylesterase, Oxidoreductases
#2: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EEE / ETHYL ACETATE


Mass: 88.105 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H8O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1057 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsTHE C1 CARBON OF EEE BECOMES SP3 RATHER THAN SP2 UPON REACTION WITH SER94. O1 BECOMES SINGLE BONDED ...THE C1 CARBON OF EEE BECOMES SP3 RATHER THAN SP2 UPON REACTION WITH SER94. O1 BECOMES SINGLE BONDED AND ACQUIRES A NEGATIVE CHARGE

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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: 2.14 Å3/Da / Density % sol: 42.7 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.7 M ammonium phosphate, 0.1 M Na,K phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 27, 2005 / Details: double crystal monochrometer
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.9→48.1 Å / Num. all: 231042 / Num. obs: 231042 / % possible obs: 96.5 % / Redundancy: 2.62 % / Biso Wilson estimate: 23.2 Å2 / Rsym value: 0.056 / Net I/σ(I): 10.5
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.54 % / Mean I/σ(I) obs: 3 / Num. unique all: 22477 / Rsym value: 0.313 / % possible all: 93.5

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Processing

Software
NameVersionClassification
CBASSdata collection
Omodel building
REFMAC5.4.0069refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VA4

1va4


Resolution: 1.9→48.1 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.664 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2124 11625 5 %RANDOM
Rwork0.19001 ---
obs0.19113 219350 96.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.529 Å2
Baniso -1Baniso -2Baniso -3
1--1.03 Å2-0.51 Å20 Å2
2---1.03 Å20 Å2
3---1.54 Å2
Refinement stepCycle: LAST / Resolution: 1.9→48.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12888 0 250 1057 14195
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02213448
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.931.96518275
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.68451682
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.88924.058626
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.884152135
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8191574
X-RAY DIFFRACTIONr_chiral_restr0.0710.21979
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02110271
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3611.58159
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.7213140
X-RAY DIFFRACTIONr_scbond_it1.08435289
X-RAY DIFFRACTIONr_scangle_it1.8814.55102
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A1068medium positional0.10.5
B1068medium positional0.10.5
C1068medium positional0.090.5
D1068medium positional0.070.5
E1068medium positional0.110.5
F1068medium positional0.150.5
A983loose positional0.375
B983loose positional0.35
C983loose positional0.265
D983loose positional0.275
E983loose positional0.295
F983loose positional0.325
A1068medium thermal0.452
B1068medium thermal0.622
C1068medium thermal0.342
D1068medium thermal0.292
E1068medium thermal0.412
F1068medium thermal0.422
A983loose thermal0.4610
B983loose thermal0.610
C983loose thermal0.3710
D983loose thermal0.3510
E983loose thermal0.4710
F983loose thermal0.4510
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 829 -
Rwork0.289 15794 -
obs--93.6 %

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