[English] 日本語
Yorodumi
- PDB-3pfc: Crystal structure of the Lactobacillus johnsonii cinnamoyl estera... -

+
Open data


ID or keywords:

Loading...

-
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 / 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
Non-polymers , 5 types, 230 molecules

#2: Chemical ChemComp-FER / 3-(4-HYDROXY-3-METHOXYPHENYL)-2-PROPENOIC 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


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


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


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more