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- PDB-3cn7: Crystal Structure Analysis of the Carboxylesterase PA3859 from Ps... -

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Basic information

Entry
Database: PDB / ID: 3cn7
TitleCrystal Structure Analysis of the Carboxylesterase PA3859 from Pseudomonas aeruginosa PAO1- MONOCLINIC CRYSTAL FORM
ComponentsCarboxylesterase
KeywordsHYDROLASE / alpha/beta hydrolase fold super-family
Function / homologyPhospholipase/carboxylesterase/thioesterase / Phospholipase/Carboxylesterase / carboxylic ester hydrolase activity / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Carboxylesterase
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsPesaresi, A. / Lamba, D.
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: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 30, 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_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_conn.pdbx_leaving_atom_flag / _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
C: Carboxylesterase
D: Carboxylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,2706
Polymers98,8804
Non-polymers3902
Water1,69394
1
A: Carboxylesterase


Theoretical massNumber of molelcules
Total (without water)24,7201
Polymers24,7201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Carboxylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9152
Polymers24,7201
Non-polymers1951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Carboxylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9152
Polymers24,7201
Non-polymers1951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Carboxylesterase


Theoretical massNumber of molelcules
Total (without water)24,7201
Polymers24,7201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.649, 50.548, 142.548
Angle α, β, γ (deg.)90.00, 92.94, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Carboxylesterase


Mass: 24719.916 Da / Num. of mol.: 4
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-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.39 Å3/Da / Density % sol: 48.51 %
Crystal growTemperature: 293 K / pH: 6.5
Details: 0.200 M AMS, 0.100 M MES, 30% w/v PEGMME-5000, Long needles grew within 3 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: 1.2
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 31, 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: 1.2 Å / Relative weight: 1
ReflectionResolution: 2.98→24.3 Å / Num. obs: 18803 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 56.8 Å2 / Rmerge(I) obs: 0.16 / Rsym value: 0.13 / Net I/σ(I): 3.9
Reflection shellResolution: 2.98→3 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 1.7 / Rsym value: 0.36 / % possible all: 98.3

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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: 2.99→23.82 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 550394.57 / 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
Rfree0.274 1849 9.8 %RANDOM
Rwork0.204 ---
obs0.204 18803 97.5 %-
all-18812 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 21.77 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 32 Å2
Baniso -1Baniso -2Baniso -3
1--6.79 Å20 Å2-2.14 Å2
2--1.44 Å20 Å2
3---5.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.65 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.99→23.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6584 0 22 94 6700
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
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_d23.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.96
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it5.8061.5
X-RAY DIFFRACTIONc_mcangle_it8.1732
X-RAY DIFFRACTIONc_scbond_it8.4952
X-RAY DIFFRACTIONc_scangle_it10.8382.5
Refine LS restraints NCSNCS model details: RESTRAIN
LS refinement shellResolution: 2.99→3.18 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.369 285 9.5 %
Rwork0.291 2708 -
obs--94.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5MES.PARMES.TOP

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