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- PDB-3cn9: Crystal Structure Analysis of the Carboxylesterase PA3859 from Ps... -

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Basic information

Entry
Database: PDB / ID: 3cn9
TitleCrystal Structure Analysis of the Carboxylesterase PA3859 from Pseudomonas aeruginosa PAO1- orthorhombic crystal form
ComponentsCarboxylesterase
KeywordsHYDROLASE / alpha/beta hydrolase fold super-family
Function / homology
Function and homology information


carboxylic ester hydrolase activity
Similarity search - Function
: / Phospholipase/carboxylesterase/thioesterase / Phospholipase/Carboxylesterase / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsLamba, D. / Pesaresi, A.
Citation
Journal: Biochimie / Year: 2010
Title: Insights into the fatty acid chain length specificity of the carboxylesterase PA3859 from Pseudomonas aeruginosa: A combined structural, biochemical and computational study.
Authors: Pesaresi, A. / Lamba, D.
#1: Journal: CURR.MICROBIOL. / Year: 2005
Title: Isolation, Characterization, and Heterologous Expression of a Carboxylesterase of Pseudomonas aeruginosa PAO1
Authors: Pesaresi, A. / Devescovi, G. / Lamba, D. / Venturi, V. / Degrassi, G.
#2: Journal: BIOCHEM.BIOPHYS.ACTA PROTEINS & PROTEOMICS / Year: 2005
Title: Crystallization, X-ray Diffraction Analysis and Phasing of Carboxylesterase PA3859 from Pseudomonas aeruginosa
Authors: Pesaresi, A. / Lamba, D.
History
DepositionMar 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 3, 2011Group: Database references
Revision 1.3Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.4Aug 30, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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

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Assembly

Deposited unit
A: Carboxylesterase
B: Carboxylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3895
Polymers49,4402
Non-polymers9493
Water5,386299
1
A: Carboxylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2553
Polymers24,7201
Non-polymers5352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Carboxylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1342
Polymers24,7201
Non-polymers4141
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.423, 96.363, 68.044
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Carboxylesterase


Mass: 24719.916 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA3859 / Plasmid: pQE-31 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 (pREP4) / References: UniProt: Q9HXE7, carboxylesterase
#2: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#3: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 3.2 Å3/Da / Density % sol: 61.53 %
Crystal growTemperature: 293 K / pH: 6.5
Details: 200mM AMS, 100 mM MES, 30% w/v PEG-MME 5000, squared bipyramids appeared within 7 to 10 days, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.278
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 25, 2002 / Details: THREE-SEGMENT PT-COATED TOROIDAL MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL (SI111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.278 Å / Relative weight: 1
ReflectionResolution: 2.09→29.05 Å / Num. obs: 36106 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 32.6 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.06 / Net I/σ(I): 6.4
Reflection shellResolution: 2.09→2.1 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2 / Rsym value: 0.39 / % possible all: 90.5

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Processing

Software
NameVersionClassification
MAR345data collection
AMoREphasing
CNS1.2refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AUO, CHAIN A

1auo


Resolution: 2.09→29.05 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1173999.84 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.24 3602 10 %RANDOM
Rwork0.196 ---
obs0.196 36106 95.5 %-
all-36512 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 76.92 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 32.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å20 Å2
2--1.88 Å20 Å2
3----2.07 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.09→29.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3292 0 64 299 3655
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.94
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.4221.5
X-RAY DIFFRACTIONc_mcangle_it3.0862
X-RAY DIFFRACTIONc_scbond_it4.0512
X-RAY DIFFRACTIONc_scangle_it5.2752.5
LS refinement shellResolution: 2.09→2.22 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.289 526 10.1 %
Rwork0.222 4686 -
obs--83.3 %

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