[English] 日本語
Yorodumi
- PDB-5yae: Ferulic acid esterase from Streptomyces cinnamoneus at 2.4 A reso... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5yae
TitleFerulic acid esterase from Streptomyces cinnamoneus at 2.4 A resolution
ComponentsEsterase
KeywordsHYDROLASE / Ferulic acid esterase / Catalytic triad / Serine protease
Function / homology
Function and homology information


1-alkyl-2-acetylglycerophosphocholine esterase activity / lipid catabolic process
Similarity search - Function
Platelet-activating factor acetylhydrolase, isoform II / Cutinase / PET hydrolase-like / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
ACETATE ION / Esterase
Similarity search - Component
Biological speciesStreptomyces cinnamoneus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsTamura, H. / Uraji, M. / Mizohata, E. / Ogawa, K. / Inoue, T. / Hatanaka, T.
CitationJournal: Appl. Environ. Microbiol. / Year: 2018
Title: Loop of Streptomyces Feruloyl Esterase Plays an Important Role in the Enzyme's Catalyzing the Release of Ferulic Acid from Biomass.
Authors: Uraji, M. / Tamura, H. / Mizohata, E. / Arima, J. / Wan, K. / Ogawa, K. / Inoue, T. / Hatanaka, T.
History
DepositionAug 31, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.title / _citation.year
Revision 1.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4716
Polymers37,0651
Non-polymers4065
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-11 kcal/mol
Surface area14320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.270, 71.290, 87.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Esterase


Mass: 37065.191 Da / Num. of mol.: 1 / Fragment: UNP residues 42-383 / Mutation: P8A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces cinnamoneus (bacteria) / Gene: estA / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0M4UW33, feruloyl esterase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: ammonium sulfate, sodium cacodylate trihydrate (pH 6.5), PEG 8000, glycerol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 2.7 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.7 Å / Relative weight: 1
ReflectionResolution: 2.34→55.32 Å / Num. obs: 14597 / % possible obs: 93.9 % / Redundancy: 30.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 42.9
Reflection shellResolution: 2.4→2.47 Å / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 10.6 / % possible all: 87.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
XSCALEdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→55.32 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.909 / SU B: 6.497 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.566 / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22026 629 4.8 %RANDOM
Rwork0.1805 ---
obs0.18248 12536 96.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.458 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å2-0 Å2
2--0 Å20 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 2.4→55.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2593 0 23 94 2710
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192685
X-RAY DIFFRACTIONr_bond_other_d0.0020.022572
X-RAY DIFFRACTIONr_angle_refined_deg1.3551.9783662
X-RAY DIFFRACTIONr_angle_other_deg0.94235903
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3795341
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.64421.593113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.72715410
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3111533
X-RAY DIFFRACTIONr_chiral_restr0.070.2401
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213039
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02608
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8221.5761363
X-RAY DIFFRACTIONr_mcbond_other0.8221.5731360
X-RAY DIFFRACTIONr_mcangle_it1.4832.3561700
X-RAY DIFFRACTIONr_mcangle_other1.4832.3561701
X-RAY DIFFRACTIONr_scbond_it0.9311.7391322
X-RAY DIFFRACTIONr_scbond_other0.9311.7411323
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.6282.5571962
X-RAY DIFFRACTIONr_long_range_B_refined2.97418.3122868
X-RAY DIFFRACTIONr_long_range_B_other2.97218.3132863
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 42 -
Rwork0.214 820 -
obs--87.69 %

+
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