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- PDB-3pf8: Crystal structure of the Lactobacillus johnsonii cinnamoyl estera... -

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Basic information

Entry
Database: PDB / ID: 3pf8
TitleCrystal structure of the Lactobacillus johnsonii cinnamoyl esterase LJ0536
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 / 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
Biological speciesLactobacillus johnsonii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.34 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 1.2Sep 6, 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_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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)60,1225
Polymers60,0532
Non-polymers693
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-24 kcal/mol
Surface area18810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.899, 149.899, 130.309
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Cinnamoyl esterase


Mass: 30026.502 Da / Num. of mol.: 2
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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.35 Å3/Da / Density % sol: 47.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M MES pH 6, 20% PEG10K, 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: 2.35→50 Å / Num. all: 23389 / Num. obs: 23389 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Biso Wilson estimate: 58.06 Å2 / Rsym value: 0.105 / Net I/σ(I): 13.44
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique allRsym valueDiffraction-ID% possible all
2.35-2.395.74.8111500.4421100
2.39-2.435.75.3811760.3771100
2.43-2.485.85.611810.3641100
2.48-2.535.86.0911650.3281100
2.53-2.595.96.8311640.282199.9
2.59-2.6567.2911730.2561100
2.65-2.716.17.711710.2341100
2.71-2.796.18.3411760.211100
2.79-2.876.28.7411620.1821100
2.87-2.966.2911750.1711100
2.96-3.076.310.1211830.155199.8
3.07-3.196.410.2111610.143199.5
3.19-3.336.410.3911860.139199.4
3.33-3.516.210.9811600.128198.9
3.51-3.735.911.4711240.117194.9
3.73-4.026.312.8911560.11198.6
4.02-4.426.313.1611710.101197.2
4.42-5.066.314.3611470.093196.9
5.06-6.376.718.3111980.085199.5
6.37-506.318.6412100.058196.3

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
BUSTER2.8.0refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB code 2WTN poly-alanine model

2wtn


Resolution: 2.34→31.49 Å / Cor.coef. Fo:Fc: 0.9182 / Cor.coef. Fo:Fc free: 0.8376 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2992 1194 5.11 %RANDOM
Rwork0.2233 ---
obs0.2271 23386 --
Displacement parametersBiso mean: 56.29 Å2
Baniso -1Baniso -2Baniso -3
1-0.5093 Å20 Å20 Å2
2--0.5093 Å20 Å2
3----1.0187 Å2
Refine analyzeLuzzati coordinate error obs: 0.404 Å
Refinement stepCycle: LAST / Resolution: 2.34→31.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3836 0 3 146 3985
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0139122
X-RAY DIFFRACTIONt_angle_deg1.2353202
X-RAY DIFFRACTIONt_dihedral_angle_d13322
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes1162
X-RAY DIFFRACTIONt_gen_planes5695
X-RAY DIFFRACTIONt_it391220
X-RAY DIFFRACTIONt_nbd15
X-RAY DIFFRACTIONt_omega_torsion2.49
X-RAY DIFFRACTIONt_other_torsion21.54
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion5245
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact46634
LS refinement shellResolution: 2.34→2.44 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.3654 140 5.29 %
Rwork0.2733 2506 -
all0.2781 2646 -
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)
11.1062-0.18580.23731.4455-0.22261.1853-0.03380.1592-0.10930.08460.0579-0.2176-0.00760.115-0.0241-0.010600.01780.1122-0.0232-0.237920.714317.151135.6343
20.5169-0.95610.21621.7611-0.7810.799-0.066-0.0749-0.23660.24530.04790.0699-0.0476-0.18250.01810.04410.04060.03140.18490.0513-0.231412.684510.804648.2312
30.3612-0.28970.15182.0174-0.72420.1388-0.0650.10210.0654-0.32380.10380.0926-0.01020.0419-0.03880.1115-0.0805-0.02050.12280.0124-0.26489.707629.815915.1326
40.1741-0.2960.4070.70840.17010.00150.00860.084-0.0584-0.12880.05020.45160.169-0.0646-0.05870.0789-0.0532-0.09230.05990.1222-0.135-5.895833.369712.4356
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|-5 - A|179 }A-5 - 179
2X-RAY DIFFRACTION2{ A|180 - A|245 }A180 - 245
3X-RAY DIFFRACTION3{ B|2 - B|179 }B2 - 179
4X-RAY DIFFRACTION4{ B|180 - B|245 }B180 - 245

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