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- PDB-3ia2: Pseudomonas fluorescens esterase complexed to the R-enantiomer of... -

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Basic information

Entry
Database: PDB / ID: 3ia2
TitlePseudomonas fluorescens esterase complexed to the R-enantiomer of a sulfonate transition state analog
ComponentsArylesterase
KeywordsHYDROLASE / alpha-beta hydrolase fold / transition state analog / 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
(2R)-butane-2-sulfonate / Arylesterase
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsSchrag, J.D. / Kazlauskas, R.J. / Jiang, Y. / Morley, K.
CitationJournal: Chembiochem / Year: 2011
Title: Different active-site loop orientation in serine hydrolases versus acyltransferases.
Authors: Jiang, Y. / Morley, K.L. / Schrag, J.D. / Kazlauskas, R.J.
History
DepositionJul 13, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 14, 2011Group: Database references
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)183,56942
Polymers179,9646
Non-polymers3,60636
Water25,5631419
1
A: Arylesterase
B: Arylesterase
C: Arylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,78721
Polymers89,9823
Non-polymers1,80518
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8280 Å2
ΔGint-41 kcal/mol
Surface area27790 Å2
MethodPISA
2
D: Arylesterase
E: Arylesterase
F: Arylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,78321
Polymers89,9823
Non-polymers1,80118
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8280 Å2
ΔGint-37 kcal/mol
Surface area27740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.215, 146.215, 129.964
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

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 6 / Auth seq-ID: 1 - 271 / Label seq-ID: 1 - 271

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF

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Components

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


Mass: 29993.955 Da / Num. of mol.: 6
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-J6Z / (2R)-butane-2-sulfonate


Mass: 137.177 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H9O3S
#3: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1419 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.46 Å3/Da / Density % sol: 72.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.7 M ammonium sulfate, 3% PEG 400, 100 mM sodium-potassium phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 21, 2005 / Details: SI(111) MONOCHROMATOR
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.65→48.57 Å / Num. all: 373997 / Num. obs: 364141 / % possible obs: 97.4 % / Redundancy: 3.65 % / Rsym value: 0.056 / Net I/σ(I): 13.2
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 2.57 % / Mean I/σ(I) obs: 3 / Rsym value: 0.343 / % possible all: 91.2

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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: 1.65→48.57 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.712 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20797 18410 5.1 %RANDOM
Rwork0.19711 ---
obs0.19766 345685 97.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.959 Å2
Baniso -1Baniso -2Baniso -3
1--1.07 Å2-0.54 Å20 Å2
2---1.07 Å20 Å2
3---1.61 Å2
Refinement stepCycle: LAST / Resolution: 1.65→48.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12720 0 217 1419 14356
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.02213585
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.7751.96218452
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.28651710
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.49924.099627
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.607152173
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8671574
X-RAY DIFFRACTIONr_chiral_restr0.0610.22017
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02110414
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_it0.2891.58283
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.565213348
X-RAY DIFFRACTIONr_scbond_it0.85935302
X-RAY DIFFRACTIONr_scangle_it1.4874.55086
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 / Number: 1993 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Aloose positional0.245
Bloose positional0.275
Cloose positional0.215
Dloose positional0.185
Eloose positional0.215
Floose positional0.295
Aloose thermal1.4610
Bloose thermal1.0310
Cloose thermal0.7410
Dloose thermal0.510
Eloose thermal1.4110
Floose thermal1.2910
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 1263 -
Rwork0.31 23296 -
obs--88.59 %

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