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- PDB-3pfb: Crystal structure of the Lactobacillus johnsonii cinnamoyl estera... -

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Basic information

Entry
Database: PDB / ID: 3pfb
TitleCrystal structure of the Lactobacillus johnsonii cinnamoyl esterase LJ0536 S106A mutant in complex with ethylferulate
ComponentsCinnamoyl esterase
KeywordsHYDROLASE / alpha/beta hydrolase fold / esterase / cinnamoyl/feruloyl esterase / hydroxycinammates / extracellular
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / aminopeptidase activity
Similarity search - Function
Serine aminopeptidase, S33 / Serine aminopeptidase, S33 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
AMMONIUM ION / Chem-ZYC / Cinnamoyl esterase
Similarity search - Component
Biological speciesLactobacillus johnsonii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsStogios, P.J. / Lai, K.K. / Vu, C. / Xu, X. / Cui, H. / Molloy, S. / Gonzalez, C.F. / Yakunin, A. / Savchenko, A.
CitationJournal: Plos One / Year: 2011
Title: An Inserted alpha/beta Subdomain Shapes the Catalytic Pocket of Lactobacillus johnsonii Cinnamoyl Esterase
Authors: Lai, K.K. / Stogios, P.J. / Vu, C. / Xu, X. / Cui, H. / Molloy, S. / Savchenko, A. / Yakunin, A. / Gonzalez, C.F.
History
DepositionOct 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2012Group: Database references
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cinnamoyl esterase
B: Cinnamoyl esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,89624
Polymers60,0212
Non-polymers87522
Water16,340907
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.260, 83.891, 88.947
Angle α, β, γ (deg.)90.00, 98.21, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Cinnamoyl esterase


Mass: 30010.502 Da / Num. of mol.: 2 / Mutation: S106A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus johnsonii (bacteria) / Gene: LJ0536 / Plasmid: p15TV-L / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: D3YEX6, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases
#2: Chemical
ChemComp-NH4 / AMMONIUM ION / Ammonium


Mass: 18.038 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: H4N
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ZYC / ethyl (2E)-3-(4-hydroxy-3-methoxyphenyl)prop-2-enoate / ethyl ferulate


Mass: 222.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H14O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 907 / 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: 2.22 Å3/Da / Density % sol: 44.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris pH 8.5, 0.2 M ammonium sulphate, 25% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Dec 15, 2009 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.58→50 Å / Num. all: 52487 / Num. obs: 52487 / % possible obs: 73.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2 % / Rsym value: 0.046 / Net I/σ(I): 31.21
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique allRsym valueDiffraction-ID% possible all
1.58-1.611.33.097690.26121.6
1.61-1.641.43.7110880.267130.3
1.64-1.671.44.714120.22139.6
1.67-1.71.55.6717720.194149.8
1.7-1.741.6721580.175160.2
1.74-1.781.88.7126990.153175.1
1.78-1.82211.3130250.132184.4
1.82-1.872.113.5229860.116183.8
1.87-1.93216.2630090.097184
1.93-1.992.119.3429690.085182.7
1.99-2.062.122.8429890.072183.3
2.06-2.142.125.5229970.066183.2
2.14-2.242.127.6329700.06183.5
2.24-2.362.128.930780.057185.6
2.36-2.512.130.8430620.052184.8
2.51-2.72.132.4630880.047186.3
2.7-2.972.134.0931140.045186
2.97-3.42.136.5630690.04185.2
3.4-4.292.138.2830900.037185.3
4.29-502.139.331430.034185.3

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Crystal structure of the Lactobacillus johnsonii cinnamoyl esterase LJ0536 S106A mutant

Resolution: 1.58→44.2 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.865 / SU B: 6.68 / SU ML: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30439 2673 5.1 %RANDOM
Rwork0.2113 ---
obs0.21609 49803 73.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.599 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å2-0 Å20.04 Å2
2---1.61 Å20 Å2
3---0.97 Å2
Refinement stepCycle: LAST / Resolution: 1.58→44.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3908 0 52 907 4867
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0224057
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9331.9655519
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.865510
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.6625.124201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.0515660
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6681518
X-RAY DIFFRACTIONr_chiral_restr0.1280.2621
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213140
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6981.52498
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.39324036
X-RAY DIFFRACTIONr_scbond_it4.28531559
X-RAY DIFFRACTIONr_scangle_it5.7084.51477
X-RAY DIFFRACTIONr_rigid_bond_restr2.26834057
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.58→1.621 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 64 -
Rwork0.302 1170 -
obs--23.5 %
Refinement TLS params.

L11: 0 °2 / L12: 0 °2 / L13: 0 °2 / L22: 0 °2 / L23: 0 °2 / L33: 0 °2 / S11: 0 Å ° / S12: 0 Å ° / S13: 0 Å ° / S21: 0 Å ° / S22: 0 Å ° / S23: 0 Å ° / S31: 0 Å ° / S32: 0 Å ° / S33: -0 Å ° / T11: 0 Å2 / T12: 0 Å2 / T13: 0 Å2 / T22: 0 Å2 / T23: 0 Å2 / T33: 0 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDOrigin x (Å)Origin y (Å)Origin z (Å)
156.258155.284912.7899
255.596428.758931.776
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-4 - 243
2X-RAY DIFFRACTION2B-4 - 329

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