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- PDB-1va4: Pseudomonas fluorescens aryl esterase -

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Basic information

Entry
Database: PDB / ID: 1va4
TitlePseudomonas fluorescens aryl esterase
ComponentsArylesterase
KeywordsHYDROLASE / alpha/beta hydrolase / esterase / non-cofactor dependent haloperoxidase
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
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.804 Å
AuthorsCheeseman, J.D. / Tocilj, A. / Park, S. / Schrag, J.D. / Kazlauskas, R.J.
CitationJournal: 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
DepositionFeb 11, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 6, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 25, 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_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

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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)187,64426
Polymers185,8026
Non-polymers1,84220
Water24,5361362
1
A: Arylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2434
Polymers30,9671
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Arylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3355
Polymers30,9671
Non-polymers3684
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Arylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2434
Polymers30,9671
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Arylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2434
Polymers30,9671
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Arylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2434
Polymers30,9671
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Arylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3355
Polymers30,9671
Non-polymers3684
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)146.040, 146.040, 129.880
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


Mass: 30966.955 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Strain: SIK WI / Plasmid: pUE1251 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5-alpha / References: UniProt: P22862, arylesterase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 1362 / 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: 4.3 Å3/Da / Density % sol: 71.41 %
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: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Apr 15, 2003 / Details: Osmic mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→48.8 Å / Num. all: 285139 / Num. obs: 271452 / % possible obs: 95.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.04 % / Rsym value: 0.066 / Net I/σ(I): 14
Reflection shellResolution: 1.804→1.851 Å / Redundancy: 2.43 % / Mean I/σ(I) obs: 3.7 / Num. unique all: 1314 / Rsym value: 0.247 / % possible all: 65.8

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
CrystalClear(MSC/RIGAKU)data reduction
d*TREKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A8S

1a8s


Resolution: 1.804→48.53 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.77 / SU ML: 0.052 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.089 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.202 27113 10 %RANDOM
Rwork0.175 ---
all-285139 --
obs-271452 95.15 %-
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 mean: 18.672 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.804→48.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12714 0 120 1362 14196
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.02113126
X-RAY DIFFRACTIONr_angle_refined_deg1.591.9517764
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.55351620
X-RAY DIFFRACTIONr_chiral_restr0.1320.21932
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0210044
X-RAY DIFFRACTIONr_nbd_refined0.2140.26639
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.21219
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1490.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1250.211
X-RAY DIFFRACTIONr_mcbond_it0.8521.58046
X-RAY DIFFRACTIONr_mcangle_it1.489212888
X-RAY DIFFRACTIONr_scbond_it2.72935080
X-RAY DIFFRACTIONr_scangle_it4.2734.54876
LS refinement shellResolution: 1.804→1.851 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.343 1314
Rwork0.317 11847

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