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- PDB-3hi4: Switching catalysis from hydrolysis to perhydrolysis in P. fluore... -

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Basic information

Entry
Database: PDB / ID: 3hi4
TitleSwitching catalysis from hydrolysis to perhydrolysis in P. fluorescens esterase
ComponentsArylesterase
KeywordsHYDROLASE / esterase / hydrolysis / perhydrolysis / 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
ACETATE ION / Arylesterase
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsPurpero, V.M.
CitationJournal: Biochemistry / Year: 2010
Title: Switching catalysis from hydrolysis to perhydrolysis in Pseudomonas fluorescens esterase.
Authors: Yin, D.L.T. / Bernhardt, P. / Morley, K.L. / Jiang, Y. / Cheeseman, J.D. / Purpero, V. / Schrag, J.D. / Kazlauskas, R.J.
History
DepositionMay 18, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 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_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
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)182,78041
Polymers179,8676
Non-polymers2,91335
Water18,6641036
1
A: Arylesterase
B: Arylesterase
C: Arylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,37920
Polymers89,9343
Non-polymers1,44517
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8560 Å2
ΔGint-38 kcal/mol
Surface area27800 Å2
MethodPISA
2
D: Arylesterase
E: Arylesterase
F: Arylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,40121
Polymers89,9343
Non-polymers1,46718
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8990 Å2
ΔGint-31 kcal/mol
Surface area27440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.490, 145.490, 129.990
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

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


Mass: 29977.912 Da / Num. of mol.: 6 / Mutation: L29P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Plasmid: pJOE2792 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: P22862, arylesterase, Oxidoreductases
#2: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1036 / 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: 4.42 Å3/Da / Density % sol: 72.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.75M ammonium sulfate 1% PEG 400, 0.1M HEPES pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 8, 2008 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.25→39.97 Å / Num. obs: 146673 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 37.652 Å2 / Rsym value: 0.079 / Net I/σ(I): 12.3
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.15 / Num. unique all: 7291 / Rsym value: 0.356 / % possible all: 99.6

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
REFMAC6.1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VA4

1va4


Resolution: 2.25→39.97 Å / SU B: 3.939 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.147 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20158 7330 5 %RANDOM
Rwork0.16458 ---
obs0.16643 146673 99.61 %-
Displacement parametersBiso mean: 29.392 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.25→39.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12708 0 185 1036 13929
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.026
X-RAY DIFFRACTIONr_angle_refined_deg1.967
X-RAY DIFFRACTIONr_gen_planes_refined0.011
LS refinement shellResolution: 2.25→2.29 Å
RfactorNum. reflection% reflection
Rfree0.307 --
Rwork0.265 --
obs-7291 99.6 %

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