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- PDB-7ebo: Crystal structure of a feruloyl esterase LP_0796 from Lactobacill... -

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Basic information

Entry
Database: PDB / ID: 7ebo
TitleCrystal structure of a feruloyl esterase LP_0796 from Lactobacillus plantarum
ComponentsCarboxylesterase
KeywordsHYDROLASE / feruloyl esterase / Lactobacillus plantarum / carboxylesterase / catalytic triad
Function / homology
Function and homology information


carboxylesterase / lipase activity / carboxylesterase activity / membrane
Similarity search - Function
Esterase/lipase / : / Serine aminopeptidase, S33 / Serine aminopeptidase, S33 / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Biological speciesLactiplantibacillus plantarum WCFS1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsZhang, H.W. / Wang, Y.L. / Xin, F.J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31700701 and 31801475 China
CitationJournal: Int.J.Biol.Macromol. / Year: 2021
Title: A reverse catalytic triad Asp containing loop shaping a wide substrate binding pocket of a feruloyl esterase from Lactobacillus plantarum.
Authors: Zhang, H. / Wen, B. / Liu, Y. / Du, G. / Wei, X. / Imam, K.M.S.U. / Zhou, H. / Fan, S. / Wang, F. / Wang, Y. / Xin, F.
History
DepositionMar 10, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carboxylesterase
B: Carboxylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0033
Polymers55,9072
Non-polymers961
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Gel filtration analysis showed this protein is a monomer in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-22 kcal/mol
Surface area18600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.891, 74.339, 110.726
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Carboxylesterase


Mass: 27953.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactiplantibacillus plantarum WCFS1 (bacteria)
Strain: ATCC BAA-793 / NCIMB 8826 / WCFS1 / Gene: lp_0796 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F9UM18, carboxylesterase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.02 Å3/Da / Density % sol: 39.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium sulfate, 0.1 M MES pH 6.5 and 25% polyethylene glycol 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 21091 / % possible obs: 96.2 % / Redundancy: 10.6 % / Biso Wilson estimate: 36.88 Å2 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.037 / Rrim(I) all: 0.118 / Χ2: 0.794 / Net I/σ(I): 9 / Num. measured all: 223710
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.287.60.48621610.9330.1830.520.53100
2.28-2.379.30.49621640.9540.1670.5240.538100
2.37-2.4811.80.48321460.9790.1450.5040.548100
2.48-2.6112.80.41321450.9870.120.4310.645100
2.61-2.7712.70.2821580.9930.0810.2910.752100
2.77-2.99130.19521860.9940.0560.2030.932100
2.99-3.2911.80.13521600.9950.0420.1411.08199.1
3.29-3.7610.30.09420880.9940.0320.10.92395.4
3.76-4.748.80.0719360.9970.0250.0741.01886.2
2.5-49.187.40.05219470.9960.0210.0561.01482.8

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TQH

1tqh


Resolution: 2.5→49.18 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2392 839 5.19 %
Rwork0.2012 15323 -
obs0.2032 16162 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 127.61 Å2 / Biso mean: 40.0658 Å2 / Biso min: 16.42 Å2
Refinement stepCycle: final / Resolution: 2.5→49.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3776 0 5 96 3877
Biso mean--57.62 39.29 -
Num. residues----484
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033875
X-RAY DIFFRACTIONf_angle_d0.7255282
X-RAY DIFFRACTIONf_chiral_restr0.043591
X-RAY DIFFRACTIONf_plane_restr0.004693
X-RAY DIFFRACTIONf_dihedral_angle_d22.9651348
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5001-2.65670.30821530.2268240597
2.6567-2.86190.27811430.22492516100
2.8619-3.14980.29821120.22692553100
3.1498-3.60550.22831470.19832553100
3.6055-4.5420.19611280.17452599100

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