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- PDB-5o7g: The crystal structure of a highly thermostable carboxyl esterase ... -

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Basic information

Entry
Database: PDB / ID: 5o7g
TitleThe crystal structure of a highly thermostable carboxyl esterase from Bacillus coagulans
ComponentsAlpha/beta hydrolase family protein
KeywordsHYDROLASE / carboxyl esterase / lipase / alpha/beta hydrolase
Function / homologySerine aminopeptidase, S33 / Serine aminopeptidase, S33 / Alpha/Beta hydrolase fold / hydrolase activity / Lysophospholipase, alpha-beta hydrolase superfamily
Function and homology information
Biological speciesBacillus coagulans DSM 1 = ATCC 7050 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGourlay, L.J.
CitationJournal: FEBS J. / Year: 2018
Title: A stereospecific carboxyl esterase from Bacillus coagulans hosting nonlipase activity within a lipase-like fold.
Authors: De Vitis, V. / Nakhnoukh, C. / Pinto, A. / Contente, M.L. / Barbiroli, A. / Milani, M. / Bolognesi, M. / Molinari, F. / Gourlay, L.J. / Romano, D.
History
DepositionJun 8, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha/beta hydrolase family protein


Theoretical massNumber of molelcules
Total (without water)39,0251
Polymers39,0251
Non-polymers00
Water90150
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.608, 138.608, 83.770
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Alpha/beta hydrolase family protein


Mass: 39024.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus coagulans DSM 1 = ATCC 7050 (bacteria)
Gene: BF29_2874 / Plasmid: pET100D/TOPO / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: A0A0B5WSQ6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 3.3 Å3/Da / Density % sol: 63.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: PACT Premier Crystallization screen (Molecular Dimensions) condition 2-11 (20% PEG3350; 0.1M sodium citrate tribasic hydrate)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 37667 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 19.4 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 26.8
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 20.4 % / Rmerge(I) obs: 0.504 / Mean I/σ(I) obs: 7.8 / Num. unique obs: 2359 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PE6

3pe6


Resolution: 1.9→39.895 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2384 1895 5.03 %
Rwork0.2167 --
obs0.2178 37654 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→39.895 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2457 0 0 50 2507
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012527
X-RAY DIFFRACTIONf_angle_d0.9963432
X-RAY DIFFRACTIONf_dihedral_angle_d13.641467
X-RAY DIFFRACTIONf_chiral_restr0.059357
X-RAY DIFFRACTIONf_plane_restr0.006450
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9001-1.94760.32781230.26942487X-RAY DIFFRACTION99
1.9476-2.00030.26631290.26782501X-RAY DIFFRACTION99
2.0003-2.05910.29111380.2652483X-RAY DIFFRACTION99
2.0591-2.12560.33481430.26012517X-RAY DIFFRACTION99
2.1256-2.20160.31981370.25872506X-RAY DIFFRACTION99
2.2016-2.28970.28691370.25592513X-RAY DIFFRACTION100
2.2897-2.39390.30911380.2482521X-RAY DIFFRACTION100
2.3939-2.52010.28411260.25072555X-RAY DIFFRACTION100
2.5201-2.67790.28871310.24042537X-RAY DIFFRACTION100
2.6779-2.88470.25151430.23882552X-RAY DIFFRACTION100
2.8847-3.17480.25791310.22972576X-RAY DIFFRACTION100
3.1748-3.6340.2041190.19982618X-RAY DIFFRACTION100
3.634-4.57740.16291410.16982619X-RAY DIFFRACTION100
4.5774-39.90340.1771590.16182774X-RAY DIFFRACTION100
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)
10.7256-0.1101-0.09770.41710.08260.2873-0.04090.09050.06720.050.0843-0.0716-0.09540.3431-0.04080.117-0.0093-0.02930.33270.0480.1765-30.2534-28.9309-14.3078
21.0852-0.01090.02880.3341-0.17870.150.03930.1498-0.0687-0.01930.0447-0.06550.03850.1946-0.06320.12030.0809-0.02740.38210.00560.1648-26.5767-43.1038-14.5902
32.55691.42620.97820.7980.55110.3892-0.00440.09740.0105-0.05620.0853-0.1291-0.09840.2217-0.03570.21760.02450.00060.6596-0.02670.2969-16.438-43.5723-31.6374
40.8475-0.6378-0.02811.2615-0.68960.65320.0230.1347-0.0773-0.1634-0.0113-0.01090.10560.01680.00170.21150.0224-0.00930.25760.04020.1894-35.8907-41.4075-36.408
50.6489-0.4024-0.07960.30330.05830.01140.02630.12510.0316-0.08570.0071-0.06510.01620.1021-0.00160.1340.0110.0020.55390.01940.2715-20.298-37.8216-25.5078
60.0655-0.0247-0.02080.08360.05090.0777-0.0010.01-0.02430.01210.034-0.05540.0650.0887-0.00640.05010.22-0.0220.26710.05950.1414-32.9523-52.2817-14.6668
70.5986-0.25310.28540.5843-0.24720.395-0.06840.0112-0.00020.02130.03060.0457-0.0756-0.02810.02390.12450.0462-0.00060.23460.02990.1652-41.8539-46.0512-20.9447
81.4169-0.11770.26581.6644-0.65962.5367-0.0118-0.119-0.03390.0650.03520.1249-0.0164-0.2267-0.03250.11850.09410.00930.17760.06030.2015-47.0317-39.8516-12.2927
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 102 )
2X-RAY DIFFRACTION2chain 'A' and (resid 103 through 158 )
3X-RAY DIFFRACTION3chain 'A' and (resid 159 through 178 )
4X-RAY DIFFRACTION4chain 'A' and (resid 179 through 203 )
5X-RAY DIFFRACTION5chain 'A' and (resid 204 through 226 )
6X-RAY DIFFRACTION6chain 'A' and (resid 227 through 269 )
7X-RAY DIFFRACTION7chain 'A' and (resid 270 through 292 )
8X-RAY DIFFRACTION8chain 'A' and (resid 293 through 309 )

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