[English] 日本語
Yorodumi
- PDB-7z2u: Wild-type ferulic acid esterase from Lactobacillus buchneri in co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7z2u
TitleWild-type ferulic acid esterase from Lactobacillus buchneri in complex with ferulate
ComponentsFerulic acid esterase
KeywordsHYDROLASE / Ferulic acid esterase / Lactobacillus buchneri / wild type / ligand
Function / homology: / feruloyl esterase / feruloyl esterase activity / Serine aminopeptidase, S33 / Serine aminopeptidase, S33 / Alpha/Beta hydrolase fold / metal ion binding / 3-(4-HYDROXY-3-METHOXYPHENYL)-2-PROPENOIC ACID / Ferulic acid esterase
Function and homology information
Biological speciesLentilactobacillus buchneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsMogodiniyai, K.K. / Reichenbach, T. / Kalyani, D.C. / Keskitalo, M.M. / Divne, C.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Other governmentFormas 2016-01449 Sweden
CitationJournal: Front Microbiol / Year: 2022
Title: Crystal structure of the feruloyl esterase from Lentilactobacillus buchneri reveals a novel homodimeric state.
Authors: Kasmaei, K.M. / Kalyani, D.C. / Reichenbach, T. / Jimenez-Quero, A. / Vilaplana, F. / Divne, C.
History
DepositionFeb 28, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ferulic acid esterase
B: Ferulic acid esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2388
Polymers63,3812
Non-polymers8576
Water5,999333
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Gelfiltration used to confirm assembly
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.500, 79.500, 228.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein Ferulic acid esterase


Mass: 31690.588 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lentilactobacillus buchneri (bacteria) / Gene: faeA / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli B (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): T1 / References: UniProt: D7RU28, feruloyl esterase
#2: Chemical
ChemComp-FER / 3-(4-HYDROXY-3-METHOXYPHENYL)-2-PROPENOIC ACID / FERULIC ACID


Mass: 194.184 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H10O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56.77 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M Na cacodylate pH 6.5, 0.2M Ca acetate, 18% PEG8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Nov 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.9→46.36 Å / Num. obs: 58652 / % possible obs: 99.9 % / Redundancy: 25.1 % / CC1/2: 0.998 / Net I/σ(I): 13.4
Reflection shellResolution: 1.9→2 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 5738 / CC1/2: 0.613

-
Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: L. buchneri FAE

Resolution: 1.9→46.356 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2155 2000 3.41 %
Rwork0.1785 --
obs0.1798 58639 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→46.356 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4158 0 58 333 4549
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074314
X-RAY DIFFRACTIONf_angle_d0.8035808
X-RAY DIFFRACTIONf_dihedral_angle_d16.3442506
X-RAY DIFFRACTIONf_chiral_restr0.053607
X-RAY DIFFRACTIONf_plane_restr0.005764
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.94760.37311390.32133955X-RAY DIFFRACTION100
1.9476-2.00020.29751410.27453973X-RAY DIFFRACTION100
2.0002-2.05910.291400.24963970X-RAY DIFFRACTION100
2.0591-2.12550.23241400.2383961X-RAY DIFFRACTION100
2.1255-2.20150.21411410.20954003X-RAY DIFFRACTION100
2.2015-2.28960.24821410.19273983X-RAY DIFFRACTION100
2.2896-2.39380.22971420.19034017X-RAY DIFFRACTION100
2.3938-2.520.21791410.19453998X-RAY DIFFRACTION100
2.52-2.67790.25321430.18044049X-RAY DIFFRACTION100
2.6779-2.88460.20391420.18014026X-RAY DIFFRACTION100
2.8846-3.17490.19691440.18124082X-RAY DIFFRACTION100
3.1749-3.63410.20161440.15854098X-RAY DIFFRACTION100
3.6341-4.5780.18141470.13194142X-RAY DIFFRACTION100
4.578-46.3560.19241550.15374382X-RAY DIFFRACTION100

+
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