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- PDB-4jgg: Crystal Structure of TesA -

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Basic information

Entry
Database: PDB / ID: 4jgg
TitleCrystal Structure of TesA
ComponentsEsterase TesA
KeywordsHYDROLASE / alpha/beta/alpha / lysophospholipase
Function / homology
Function and homology information


carboxylesterase / carboxylesterase activity / phosphatidylcholine lysophospholipase activity / arylesterase activity / extracellular region
Similarity search - Function
: / SGNH hydrolase / SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / SGNH hydrolase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKovacic, F. / Granzin, J. / Batra-Safferling, R. / Jaeger, K.-E.
CitationJournal: Plos One / Year: 2013
Title: Structural and Functional Characterisation of TesA - A Novel Lysophospholipase A from Pseudomonas aeruginosa.
Authors: Kovacic, F. / Granzin, J. / Wilhelm, S. / Kojic-Prodic, B. / Batra-Safferling, R. / Jaeger, K.E.
History
DepositionMar 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Esterase TesA
B: Esterase TesA


Theoretical massNumber of molelcules
Total (without water)43,7652
Polymers43,7652
Non-polymers00
Water4,972276
1
A: Esterase TesA


Theoretical massNumber of molelcules
Total (without water)21,8821
Polymers21,8821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Esterase TesA


Theoretical massNumber of molelcules
Total (without water)21,8821
Polymers21,8821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.965, 103.080, 45.888
Angle α, β, γ (deg.)90.00, 97.57, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Esterase TesA


Mass: 21882.291 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: PA2856, tesA / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HZY8, carboxylesterase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.2 Å3/Da / Density % sol: 43.97 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 20% PEG 3350, 50mM sodium-citrate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 4, 2009
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.9→45.49 Å / Num. all: 29767 / Num. obs: 29422 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 13.45 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 13
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 4.7 / Num. unique all: 1485 / Rsym value: 0.242 / % possible all: 98.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7_632)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3HP4

3hp4


Resolution: 1.9→40.625 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 28.3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2623 1478 5.03 %RANDOM
Rwork0.2268 ---
all0.2286 29767 --
obs0.2286 29407 98.79 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-13.5635 Å20 Å23.2054 Å2
2---5.5172 Å2-0 Å2
3----8.0463 Å2
Refinement stepCycle: LAST / Resolution: 1.9→40.625 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2617 0 0 276 2893
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072664
X-RAY DIFFRACTIONf_angle_d1.0163632
X-RAY DIFFRACTIONf_dihedral_angle_d12.548962
X-RAY DIFFRACTIONf_chiral_restr0.064426
X-RAY DIFFRACTIONf_plane_restr0.004480
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.96790.30471480.24132795X-RAY DIFFRACTION99
1.9679-2.04670.31861440.23612788X-RAY DIFFRACTION99
2.0467-2.13990.28851310.22322801X-RAY DIFFRACTION99
2.1399-2.25270.25681590.22272782X-RAY DIFFRACTION99
2.2527-2.39380.25161300.232781X-RAY DIFFRACTION98
2.3938-2.57860.27591180.23242778X-RAY DIFFRACTION98
2.5786-2.8380.27271650.2422763X-RAY DIFFRACTION98
2.838-3.24860.25681510.22952789X-RAY DIFFRACTION99
3.2486-4.09220.23221630.21292821X-RAY DIFFRACTION100
4.0922-40.63460.25531690.22242830X-RAY DIFFRACTION99

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