[English] 日本語
Yorodumi
- PDB-6mou: Bacteroides intestinalis feruloyl esterase, Bacint_01033 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6mou
TitleBacteroides intestinalis feruloyl esterase, Bacint_01033
ComponentsIsoamylase N-terminal domain protein
KeywordsHYDROLASE / carbohydrate esterase / feruloyl esterase
Function / homology: / Esterase-like / Putative esterase / acyltransferase activity, transferring groups other than amino-acyl groups / Immunoglobulin E-set / Alpha/Beta hydrolase fold / Immunoglobulin-like fold / Isoamylase N-terminal domain protein
Function and homology information
Biological speciesBacteroides intestinalis DSM 17393 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.24 Å
AuthorsKoropatkin, N.M. / Pereira, G.V. / Cann, I.
CitationJournal: Nat Commun / Year: 2021
Title: Degradation of complex arabinoxylans by human colonic Bacteroidetes
Authors: Pereira, G.V. / DAlessandro-Gabazza, C. / Farris, J. / Wefers, D. / Mackie, R. / Koropatkin, N.M. / Gabazza, E.C. / Cann, I.
History
DepositionOct 4, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Oct 30, 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: Isoamylase N-terminal domain protein
B: Isoamylase N-terminal domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,4356
Polymers87,1862
Non-polymers2484
Water8,017445
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-13 kcal/mol
Surface area29260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.206, 95.206, 202.609
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein Isoamylase N-terminal domain protein


Mass: 43593.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides intestinalis DSM 17393 (bacteria)
Gene: BACINT_01033 / Production host: Escherichia coli (E. coli) / References: UniProt: B3C969
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 445 / 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: 3.24 Å3/Da / Density % sol: 62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Bis-Tris pH 6.5, 20% PEG 1,500. Hampton PegRx screen well B8
Temp details: room

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryo / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.979 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 7, 2018
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.24→76.37 Å / Num. obs: 98838 / % possible obs: 100 % / Redundancy: 5.8 % / Biso Wilson estimate: 30.87 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.18 / Net I/σ(I): 7.5
Reflection shellResolution: 2.24→2.32 Å / Rmerge(I) obs: 0.78 / CC1/2: 0.573

-
Processing

Software
NameVersionClassification
d*TREKdata reduction
xia2data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.24→76.369 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.27
RfactorNum. reflection% reflection
Rfree0.236 3788 3.83 %
Rwork0.1903 --
obs0.192 98829 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 103.13 Å2 / Biso mean: 32.7476 Å2 / Biso min: 17.55 Å2
Refinement stepCycle: final / Resolution: 2.24→76.369 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5702 0 40 445 6187
Biso mean--44.53 36.02 -
Num. residues----713
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.24-2.26840.42181340.31735633697
2.2684-2.29820.36121400.307634733613
2.2982-2.32970.32071480.294335873735
2.3297-2.3630.29851400.279734383578
2.363-2.39830.31871500.270935723722
2.3983-2.43570.26881380.266935263664
2.4357-2.47570.32191300.273134303560
2.4757-2.51840.35561460.253335673713
2.5184-2.56420.29181460.25635543700
2.5642-2.61350.33061360.239934803616
2.6135-2.66680.3331360.239235383674
2.6668-2.72480.29141400.238335493689
2.7248-2.78820.2691400.226835013641
2.7882-2.85790.28821440.226935023646
2.8579-2.93520.25521400.21335383678
2.9352-3.02160.25021420.206735303672
3.0216-3.11910.27651360.197535163652
3.1191-3.23060.24571480.195635023650
3.2306-3.35990.21211340.182935273661
3.3599-3.51290.23661480.180335283676
3.5129-3.69810.21271380.162334983636
3.6981-3.92970.18981330.14835343667
3.9297-4.23310.16721420.137335033645
4.2331-4.65910.13941390.118135203659
4.6591-5.33310.18231460.128835323678
5.3331-6.71850.18091320.158335313663
6.7185-76.41380.20181420.169735023644

+
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