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- PDB-3doi: Crystal Structure of a Thermostable Esterase complex with paraoxon -

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Basic information

Entry
Database: PDB / ID: 3doi
TitleCrystal Structure of a Thermostable Esterase complex with paraoxon
Componentsesterase
KeywordsHYDROLASE / alpha-beta Hydrolase / beta sheet
Function / homology
Function and homology information


Immunoglobulin-like - #2180 / Esterase, Ig-like N-terminal / Esterase Ig-like N-terminal domain / : / Phospholipase/carboxylesterase/thioesterase / Phospholipase/Carboxylesterase / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Immunoglobulin-like / Sandwich ...Immunoglobulin-like - #2180 / Esterase, Ig-like N-terminal / Esterase Ig-like N-terminal domain / : / Phospholipase/carboxylesterase/thioesterase / Phospholipase/Carboxylesterase / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
DIETHYL PHOSPHONATE / Phospholipase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsLevisson, M. / Sun, L. / Hendriks, S. / Dijkstra, B.W. / Van der Oost, J. / Kengen, S.W.M.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Crystal structure and biochemical properties of a novel thermostable esterase containing an immunoglobulin-like domain.
Authors: Levisson, M. / Sun, L. / Hendriks, S. / Swinkels, P. / Akveld, T. / Bultema, J.B. / Barendregt, A. / van den Heuvel, R.H.H. / Dijkstra, B.W. / van der Oost, J. / Kengen, S.W.M.
History
DepositionJul 4, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: esterase
B: esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,4124
Polymers86,1362
Non-polymers2762
Water00
1
A: esterase
B: esterase
hetero molecules

A: esterase
B: esterase
hetero molecules

A: esterase
B: esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)259,23512
Polymers258,4076
Non-polymers8296
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
2
A: esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2062
Polymers43,0681
Non-polymers1381
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2062
Polymers43,0681
Non-polymers1381
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)130.542, 130.542, 304.553
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein esterase


Mass: 43067.750 Da / Num. of mol.: 2 / Fragment: residues 17-395
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: TM_0033 / Plasmid: pET-24d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9WXP0, carboxylesterase
#2: Chemical ChemComp-DEP / DIETHYL PHOSPHONATE


Mass: 138.102 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H11O3P

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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: 2.9 Å3/Da / Density % sol: 57.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG 8000, 1M lithium sulphate monohydrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 7, 2007 / Details: mirrors
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 20405 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.9 % / Rmerge(I) obs: 0.152 / Net I/σ(I): 13.4
Reflection shellResolution: 3→3.16 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.643 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→37.69 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.894 / SU B: 20.655 / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.455 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26648 1041 5.1 %RANDOM
Rwork0.2199 ---
obs0.22221 19311 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 46.551 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å2-0.31 Å20 Å2
2---0.63 Å20 Å2
3---0.94 Å2
Refinement stepCycle: LAST / Resolution: 3→37.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5982 0 16 0 5998
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0226185
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7711.9648427
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.4095745
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.36524.476286
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.267151011
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7571529
X-RAY DIFFRACTIONr_chiral_restr0.1160.2918
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024719
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.250.23061
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3290.24171
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2180.2242
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2880.265
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6961.53818
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.27126111
X-RAY DIFFRACTIONr_scbond_it1.43332697
X-RAY DIFFRACTIONr_scangle_it2.4494.52316
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 85 -
Rwork0.307 1394 -
obs--99.8 %

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