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

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Basic information

Entry
Database: PDB / ID: 3pfc
TitleCrystal structure of the Lactobacillus johnsonii cinnamoyl esterase LJ0536 S106A mutant in complex with ferulic acid
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
3-(4-HYDROXY-3-METHOXYPHENYL)-2-PROPENOIC ACID / Cinnamoyl esterase
Similarity search - Component
Biological speciesLactobacillus johnsonii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,01817
Polymers30,0111
Non-polymers1,00816
Water3,855214
1
A: Cinnamoyl esterase
hetero molecules

A: Cinnamoyl esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,03634
Polymers60,0212
Non-polymers2,01532
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area6330 Å2
ΔGint-171 kcal/mol
Surface area18810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.046, 85.402, 80.981
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cinnamoyl esterase


Mass: 30010.502 Da / Num. of mol.: 1 / 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

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Non-polymers , 5 types, 230 molecules

#2: Chemical ChemComp-FER / 3-(4-HYDROXY-3-METHOXYPHENYL)-2-PROPENOIC ACID / FERULIC ACID / Ferulic acid


Mass: 194.184 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H10O4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000 / Polyethylene glycol


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 2.07 Å3/Da / Density % sol: 40.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris pH 8.5, 0.2 M lithium sulfate, 30% PEG4K, 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: 1.75→50 Å / Num. all: 25396 / Num. obs: 25396 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Rsym value: 0.058 / Net I/σ(I): 22.2
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsRsym valueDiffraction-ID% possible all
1.75-1.785.12.880.484194
1.78-1.815.63.60.4081100
1.81-1.855.73.950.373199.8
1.85-1.895.74.550.3131100
1.89-1.935.75.030.2721100
1.93-1.975.86.040.2321100
1.97-2.025.77.770.1811100
2.02-2.075.77.70.1671100
2.07-2.145.810.390.1371100
2.14-2.25.812.970.111100
2.2-2.285.811.220.113199.8
2.28-2.385.814.940.0891100
2.38-2.485.916.710.079199.9
2.48-2.615.920.170.0671100
2.61-2.785.921.060.062199.9
2.78-2.995.925.020.049199.8
2.99-3.295.930.980.041199.9
3.29-3.775.933.050.037199.8
3.77-4.755.936.50.034199.5
4.75-505.735.140.034197.3

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
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: 1.75→17.649 Å / SU ML: 0.18 / σ(F): 0 / Phase error: 16.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1786 1245 5.01 %
Rwork0.1518 --
obs0.1531 24852 97.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.613 Å2 / ksol: 0.397 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.4346 Å20 Å20 Å2
2---1.9376 Å2-0 Å2
3---0.5031 Å2
Refinement stepCycle: LAST / Resolution: 1.75→17.649 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1954 0 34 214 2202
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0162025
X-RAY DIFFRACTIONf_angle_d1.6772752
X-RAY DIFFRACTIONf_dihedral_angle_d13.42737
X-RAY DIFFRACTIONf_chiral_restr0.12311
X-RAY DIFFRACTIONf_plane_restr0.01362
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7499-1.81990.2541230.23262391X-RAY DIFFRACTION90
1.8199-1.90260.2391340.18512534X-RAY DIFFRACTION95
1.9026-2.00280.17131370.16022582X-RAY DIFFRACTION97
2.0028-2.12810.18631360.14912613X-RAY DIFFRACTION98
2.1281-2.29210.1721400.14792629X-RAY DIFFRACTION98
2.2921-2.52220.20151420.15212668X-RAY DIFFRACTION99
2.5222-2.88580.19641420.16042671X-RAY DIFFRACTION99
2.8858-3.63050.1861430.15172710X-RAY DIFFRACTION100
3.6305-17.64990.14031480.13322809X-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)
10.55390.36650.08742.14550.76330.3038-0.0163-0.0045-0.0111-0.2326-0.11220.3349-0.0373-0.03960.11770.11220.0121-0.03750.12-0.02610.1463-27.5885-11.5703-7.3898
20.336-0.1468-0.22591.94490.95831.17680.0250.0379-0.0793-0.2860.0577-0.2101-0.01040.1578-0.07850.15230.00270.01910.1387-0.01550.1327-14.5427-18.4355-13.6151
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid -5:179
2X-RAY DIFFRACTION2chain A and resid 180:244

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