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- PDB-3t52: L29I Mutation in an Aryl Esterase from Pseudomonas fluorescens Le... -

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Basic information

Entry
Database: PDB / ID: 3t52
TitleL29I Mutation in an Aryl Esterase from Pseudomonas fluorescens Leads to Unique Peptide Flip and Increased Activity
ComponentsArylesterase
KeywordsOXIDOREDUCTASE / HYDRLOASE / peptide flip
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 / HYDROGEN PEROXIDE / Arylesterase
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsKazlauskas, R.J. / Yin, T. / Purpero, V.M.
CitationJournal: To be Published
Title: L29I Mutation in an Aryl Esterase from Pseudomonas fluorescens Leads to Unique Peptide Flip and Increased Activity
Authors: Yin, T. / Kazlauskas, R.J. / Purpero, V.M.
History
DepositionJul 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 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
Revision 1.2Apr 3, 2024Group: Refinement description / Category: 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)186,611104
Polymers179,9646
Non-polymers6,64798
Water21,0051166
1
A: Arylesterase
B: Arylesterase
C: Arylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,18351
Polymers89,9823
Non-polymers3,20148
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13650 Å2
ΔGint-104 kcal/mol
Surface area27940 Å2
MethodPISA
2
D: Arylesterase
E: Arylesterase
F: Arylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,42953
Polymers89,9823
Non-polymers3,44750
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14650 Å2
ΔGint-86 kcal/mol
Surface area27420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.020, 146.020, 128.950
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

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Protein , 1 types, 6 molecules ABCDEF

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


Mass: 29993.955 Da / Num. of mol.: 6 / Mutation: L29I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Strain: SIK WI / Plasmid: pL29I / Production host: Escherichia coli (E. coli) / Strain (production host): Dh5 alpha / References: UniProt: P22862, arylesterase, Oxidoreductases

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Non-polymers , 6 types, 1264 molecules

#2: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-PEO / HYDROGEN PEROXIDE


Mass: 34.015 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: H2O2
#6: Chemical...
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1166 / 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: 4.41 Å3/Da / Density % sol: 72.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1% PEG 400, 1.65M (NH4)2SO4, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.98 Å
DetectorType: NOIR-1 / Detector: CCD / Date: May 10, 2008 / Details: mirrors
RadiationMonochromator: Rosenbaum-Rock Si(111) sagitally focused monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→48.33 Å / Num. obs: 207756 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 3 / Redundancy: 5.46 % / Biso Wilson estimate: 22.1 Å2 / Rmerge(I) obs: 0.111 / Χ2: 0.97 / Net I/σ(I): 6.6 / Scaling rejects: 11454
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2-2.075.260.4272.9111064207711.26100
2.07-2.155.310.3243.5111878207331.21100
2.15-2.255.320.2973.9112553207981.19100
2.25-2.375.410.2524.3113272207781.03100
2.37-2.525.540.1994.9115225207620.9100
2.52-2.715.510.1745.7115174207800.96100
2.71-2.995.580.1456.6116254207840.85100
2.99-3.425.580.1118.6116820208430.77100
3.42-4.315.460.08811.9115750207440.8799.9
4.31-48.335.60.06913.7117313207630.7199.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.12 Å48.23 Å
Translation2.12 Å48.23 Å

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Processing

Software
NameVersionClassificationNB
d*TREK9.9.3Ldata scaling
d*TREK9.9.3Ldata reduction
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry IVA4

Resolution: 2→47.8 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / WRfactor Rfree: 0.223 / WRfactor Rwork: 0.1936 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8321 / SU B: 2.781 / SU ML: 0.077 / SU R Cruickshank DPI: 0.1218 / SU Rfree: 0.1171 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 3 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2108 10433 5 %RANDOM
Rwork0.1837 ---
obs0.185 207522 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 76.66 Å2 / Biso mean: 25.825 Å2 / Biso min: 12.68 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0.02 Å20 Å2
2---0.03 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 2→47.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12719 0 409 1166 14294
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02213786
X-RAY DIFFRACTIONr_angle_refined_deg1.3681.96418676
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.29151723
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.45524.114649
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.581152189
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4991577
X-RAY DIFFRACTIONr_chiral_restr0.1040.22000
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02110597
X-RAY DIFFRACTIONr_mcbond_it0.7441.58336
X-RAY DIFFRACTIONr_mcangle_it1.339213352
X-RAY DIFFRACTIONr_scbond_it2.21435450
X-RAY DIFFRACTIONr_scangle_it3.5354.55279
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0.117 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 762 -
Rwork0.243 14540 -
all-15302 -
obs-14540 99.99 %

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