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- PDB-3s2z: Crystal structure of the Lactobacillus johnsonii cinnamoyl estera... -

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Basic information

Entry
Database: PDB / ID: 3s2z
TitleCrystal structure of the Lactobacillus johnsonii cinnamoyl esterase LJ0536 S106A mutant in complex with caffeic acid
ComponentsCinnamoyl esterase
KeywordsHYDROLASE / ALPHA/BETA HYDROLASE FOLD / ESTERASE / CINNAMOYL/FERULOYL ESTERASE / HYDROXYCINAMMATES
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / carboxylic ester hydrolase 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
CAFFEIC ACID / Cinnamoyl esterase
Similarity search - Component
Biological speciesLactobacillus johnsonii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.76 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
DepositionMay 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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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)60,94920
Polymers60,0212
Non-polymers92818
Water7,782432
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5220 Å2
ΔGint-153 kcal/mol
Surface area18730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.318, 84.168, 87.604
Angle α, β, γ (deg.)90.00, 97.56, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-596-

HOH

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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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-DHC / CAFFEIC ACID / 3,4-DIHYDROXYCINNAMIC ACID


Mass: 180.157 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H8O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 432 / 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: 2.2 Å3/Da / Density % sol: 44.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M TRIS, 0.2 M LITHIUM SULPHATE, 30% PEG4K, pH 8.5, 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: 1.54178 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jan 15, 2010
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. all: 51281 / Num. obs: 51428 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Rsym value: 0.047 / Net I/σ(I): 21.86
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allRsym valueDiffraction-ID% possible all
1.75-1.783.325200.462197.6
4.75-506.426440.033199.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3PF8

3pf8


Resolution: 1.76→50 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.952 / SU B: 5.952 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20862 2615 5.1 %RANDOM
Rwork0.14258 ---
obs0.14596 48659 98.91 %-
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: 35.29 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-1.03 Å2
2---2.07 Å20 Å2
3---1.81 Å2
Refinement stepCycle: LAST / Resolution: 1.76→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3916 0 42 432 4390
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0224045
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8121.965501
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0595505
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.43225.099202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.73115653
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8771518
X-RAY DIFFRACTIONr_chiral_restr0.1320.2618
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213139
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_it1.9011.52494
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.92524026
X-RAY DIFFRACTIONr_scbond_it4.94531551
X-RAY DIFFRACTIONr_scangle_it7.0164.51472
X-RAY DIFFRACTIONr_rigid_bond_restr2.53334045
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.76→1.803 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 173 -
Rwork0.19 3179 -
obs--87.43 %
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)
123.3753-1.6329.7399
210.0994-9.363335.2647
323.677420.351214.3501
410.302627.49738.0532
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-5 - 179
2X-RAY DIFFRACTION2A180 - 245
3X-RAY DIFFRACTION3B-5 - 179
4X-RAY DIFFRACTION4B180 - 244

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