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- PDB-3qm1: CRYSTAL STRUCTURE OF THE LACTOBACILLUS JOHNSONII CINNAMOYL ESTERA... -

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Basic information

Entry
Database: PDB / ID: 3qm1
TitleCRYSTAL STRUCTURE OF THE LACTOBACILLUS JOHNSONII CINNAMOYL ESTERASE LJ0536 S106A MUTANT IN COMPLEX WITH ETHYLFERULATE, Form II
ComponentsCinnamoyl esterase
KeywordsHYDROLASE / ALPHA/BETA HYDROLASE FOLD / CINNAMOYL/FERULOYL ESTERASE / HYDROXYCINAMMATES
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
Chem-ZYC / Cinnamoyl esterase
Similarity search - Component
Biological speciesLactobacillus johnsonii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.817 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
DepositionFeb 3, 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 / 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_alt_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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 / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cinnamoyl esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,31163
Polymers29,4501
Non-polymers1,86162
Water3,117173
1
A: Cinnamoyl esterase
hetero molecules

A: Cinnamoyl esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,623126
Polymers58,9002
Non-polymers3,723124
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.872, 85.396, 81.142
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-302-

CL

21A-456-

HOH

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Components

#1: Protein Cinnamoyl esterase


Mass: 29449.943 Da / Num. of mol.: 1 / Fragment: UNP residues 22-265 / 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-ZYC / ethyl (2E)-3-(4-hydroxy-3-methoxyphenyl)prop-2-enoate / ethyl ferulate


Mass: 222.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H14O4
#3: Chemical...
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 42 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE BOND ANGLE OAL-CAM-OAC, WITH A VALUE OF 116 DEGREES, IS MODELED IN UNAMBIGUOUS ELECTRON DENSITY ...THE BOND ANGLE OAL-CAM-OAC, WITH A VALUE OF 116 DEGREES, IS MODELED IN UNAMBIGUOUS ELECTRON DENSITY TO CONTAIN PARTIAL CHIRAL CHARACTER PERHAPS DUE TO THE FACT THAT THIS LIGAND IS BOUND TO A CATALYTICALLY INACTIVE MUTANT, S106A, OF THE LJ0536 ENZYME. BOND IS STRAINED FROM IDEAL OF 120 DEGREES AS ENZYME COULD HAVE TRAPPED SUBSTRATE IN A PSEUDO-TRANSITION STATE OF THE HYDROLYSIS REACTION, PRESUMED TO CONTAIN A TETRAHEDRAL TRANSITION STATE WITH A OAL-CAM-OAC BOND ANGLE OF 109 DEGREES

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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: 2.11 Å3/Da / Density % sol: 41.81 %
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, 24% PEG3350, 25 mM ethyl ferulate, 1/10 V8 protease, 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 8, 2010 / 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: 1.82→23.8 Å / Num. all: 22853 / Num. obs: 22853 / % possible obs: 100 % / Observed criterion σ(F): 2 / Redundancy: 6.1 % / Rsym value: 0.048 / Net I/σ(I): 27.56
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsRsym valueDiffraction-ID% possible all
1.82-1.854.83.180.326199.99
1.85-1.8964.180.3011100
1.89-1.926.15.240.2471100
1.92-1.966.16.110.2161100
1.96-26.17.50.1791100
2-2.056.19.170.1471100
2.05-2.16.210.340.1381100
2.1-2.166.111.920.1171100
2.16-2.226.213.910.1021100
2.22-2.296.214.970.0941100
2.29-2.376.316.450.0851100
2.37-2.476.218.40.0761100
2.47-2.586.321.380.0661100
2.58-2.726.323.610.061100
2.72-2.896.327.780.0521100
2.89-3.116.335.670.041100
3.11-3.426.343.440.0321100
3.42-3.926.350.470.0271100
3.92-4.936.357.170.0231100
4.93-23.8654.620.0221100

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB code 3PF8

3pf8


Resolution: 1.817→23.067 Å / SU ML: 0.19 / σ(F): 0 / Phase error: 16.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1901 1119 5.01 %
Rwork0.147 --
obs0.1491 22353 97.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.33 Å2 / ksol: 0.382 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.4024 Å2-0 Å2-0 Å2
2---2.4242 Å20 Å2
3----0.9782 Å2
Refinement stepCycle: LAST / Resolution: 1.817→23.067 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1951 0 77 173 2201
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0162056
X-RAY DIFFRACTIONf_angle_d1.712809
X-RAY DIFFRACTIONf_dihedral_angle_d13.38760
X-RAY DIFFRACTIONf_chiral_restr0.116320
X-RAY DIFFRACTIONf_plane_restr0.01371
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8168-1.89940.26691330.22682505X-RAY DIFFRACTION94
1.8994-1.99950.19411350.16362560X-RAY DIFFRACTION95
1.9995-2.12470.20881370.13922608X-RAY DIFFRACTION98
2.1247-2.28860.1891410.13852631X-RAY DIFFRACTION98
2.2886-2.51860.21151380.14222666X-RAY DIFFRACTION98
2.5186-2.88250.20211400.15292688X-RAY DIFFRACTION99
2.8825-3.62940.17831450.14052740X-RAY DIFFRACTION100
3.6294-23.06860.16641500.13912836X-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)
10.40860.22830.00931.7207-0.61270.2404-0.02320.01460.0181-0.2004-0.069-0.34150.0450.01970.08790.08280.00510.0380.09230.01520.135127.48711.4229-7.4499
20.2407-0.20120.22291.8123-0.96120.98860.0260.04220.0724-0.27840.06270.15160.0905-0.1782-0.08370.1073-0.0029-0.01310.10820.0170.094614.599318.5354-13.7587
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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