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- PDB-4bzz: Complete crystal structure of carboxylesterase Cest-2923 from Lac... -

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Basic information

Entry
Database: PDB / ID: 4bzz
TitleComplete crystal structure of carboxylesterase Cest-2923 from Lactobacillus plantarum WCFS1
ComponentsLIPASE/ESTERASE
KeywordsHYDROLASE / CARBOXYLESTERASE
Function / homology
Function and homology information


aminopeptidase activity / identical protein binding / metal ion binding
Similarity search - Function
: / BD-FAE / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / ACETONITRILE / Lipase/esterase
Similarity search - Component
Biological speciesLACTOBACILLUS PLANTARUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsBenavente, R. / Esteban-Torres, M. / Acebron, I. / de las Rivas, B. / Munoz, R. / Alvarez, Y. / Mancheno, J.M.
CitationJournal: FEBS J. / Year: 2013
Title: Structure, Biochemical Characterization and Analysis of the Pleomorphism of Carboxylesterase Cest-2923 from Lactobacillus Plantarum Wcfs1
Authors: Benavente, R. / Esteban-Torres, M. / Acebron, I. / De Las Rivas, B. / Munoz, R. / Alvarez, Y. / Mancheno, J.M.
History
DepositionJul 30, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: LIPASE/ESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8789
Polymers31,2751
Non-polymers6028
Water724
1
A: LIPASE/ESTERASE
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)191,26654
Polymers187,6526
Non-polymers3,61548
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
crystal symmetry operation10_555-y,-x,-z1
crystal symmetry operation11_655-x+y+1,y,-z1
crystal symmetry operation12_545x,x-y-1,-z1
Buried area26170 Å2
ΔGint-415.7 kcal/mol
Surface area52600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.721, 140.721, 82.290
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622

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Components

#1: Protein LIPASE/ESTERASE / CEST-2923


Mass: 31275.307 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LACTOBACILLUS PLANTARUM (bacteria) / Strain: WCFS1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: F9US10, carboxylesterase
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CCN / ACETONITRILE / Acetonitrile


Mass: 41.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3N
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 3.8 Å3/Da / Density % sol: 67 % / Description: NONE
Crystal growpH: 4.6
Details: 1.7 M AMMONIUM SULPHATE, 0.15 M SODIUM ACETATE, PH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9687
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9687 Å / Relative weight: 1
ReflectionResolution: 2.99→49 Å / Num. obs: 9994 / % possible obs: 99.6 % / Redundancy: 7.5 % / Biso Wilson estimate: 52.06 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 13.7
Reflection shellResolution: 2.99→3.15 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 4.1 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB EBTRY 3D3N

3d3n


Resolution: 3→46.062 Å / SU ML: 0.26 / σ(F): 1.34 / Phase error: 19.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2078 480 4.8 %
Rwork0.152 --
obs0.1547 9984 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→46.062 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2138 0 35 4 2177
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072231
X-RAY DIFFRACTIONf_angle_d1.0423053
X-RAY DIFFRACTIONf_dihedral_angle_d15.475767
X-RAY DIFFRACTIONf_chiral_restr0.075338
X-RAY DIFFRACTIONf_plane_restr0.004394
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.4340.24191600.18623089X-RAY DIFFRACTION99
3.434-4.3260.22161600.14383124X-RAY DIFFRACTION99
4.326-46.06720.18571600.14383291X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.62430.70255.24642.08740.65744.1627-0.09130.2110.0152-0.1774-0.3288-0.0403-0.07290.49390.34110.387-0.08290.09620.4657-0.08610.386162.3491-41.969212.6666
21.16280.6494-0.05532.127-0.78543.93090.1591-0.39060.14610.1812-0.1817-0.0204-0.34130.24180.03030.2635-0.07170.04380.529-0.09920.355352.7438-46.604319.6151
32.0958-0.2784-0.61115.42390.58293.51260.2605-0.5749-0.12570.4021-0.23010.32230.1023-0.2751-0.0170.26-0.10470.05070.5438-0.03680.321541.3754-57.69922.1543
47.204-3.3148-1.86694.3942.07596.07960.26280.0164-0.6844-0.6108-0.23570.7540.4342-0.11740.11090.3288-0.0638-0.0270.4996-0.03440.273544.1688-58.46747.6933
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 1 THROUGH 21 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 22 THROUGH 183 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 184 THROUGH 239 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 240 THROUGH 275 )

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