[English] 日本語
Yorodumi
- PDB-7e29: Crystal Structure of Saccharomyces cerevisiae Ioc4 PWWP domain fu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7.0E+29
TitleCrystal Structure of Saccharomyces cerevisiae Ioc4 PWWP domain fused with MBP
ComponentsMaltose/maltodextrin-binding periplasmic protein,ISWI one complex protein 4
KeywordsGENE REGULATION / PWWP / TRANSCRIPTION
Function / homology
Function and homology information


Isw1b complex / Isw1 complex / sister chromatid cohesion / detection of maltose stimulus / maltose transport complex / maltose binding / carbohydrate transport / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity ...Isw1b complex / Isw1 complex / sister chromatid cohesion / detection of maltose stimulus / maltose transport complex / maltose binding / carbohydrate transport / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / response to heat / periplasmic space / chromatin remodeling / DNA damage response / regulation of DNA-templated transcription / membrane / nucleus
Similarity search - Function
IOC4-like, PWWP domain / domain with conserved PWWP motif / PWWP domain / PWWP domain / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
alpha-maltose / Maltose/maltodextrin-binding periplasmic protein / ISWI one complex protein 4
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.303 Å
AuthorsLi, J. / Smolle, M. / Liang, H. / Liu, Y.
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: H3K36 methylation and DNA-binding both promote Ioc4 recruitment and Isw1b remodeler function.
Authors: Li, J. / Bergmann, L. / Rafael de Almeida, A. / Webb, K.M. / Gogol, M.M. / Voigt, P. / Liu, Y. / Liang, H. / Smolle, M.M.
History
DepositionFeb 5, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 1.1May 25, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 1.2Nov 29, 2023Group: 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: Maltose/maltodextrin-binding periplasmic protein,ISWI one complex protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,6882
Polymers61,3461
Non-polymers3421
Water5,405300
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area830 Å2
ΔGint8 kcal/mol
Surface area21880 Å2
Unit cell
Length a, b, c (Å)153.303, 153.303, 42.004
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

-
Components

#1: Protein Maltose/maltodextrin-binding periplasmic protein,ISWI one complex protein 4 / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP


Mass: 61345.547 Da / Num. of mol.: 1 / Mutation: E385A, K388A, D389A
Source method: isolated from a genetically manipulated source
Details: The fusion protein of MBP (residues 2-367, UNP residues 27-392), LINKER, and ISWI one complex protein 4 (residues 374-551 , UNP residues 1-178)
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: K12, ATCC 204508 / S288c / Gene: malE, b4034, JW3994, IOC4, YMR044W, YM9532.09 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEX9, UniProt: Q04213
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: Potassium thiocyanate, Polyethylene glycol monomethyl ether 2000
PH range: 6.5 - 8.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 25377 / % possible obs: 99.9 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 35.5
Reflection shellResolution: 2.3→2.34 Å / Rmerge(I) obs: 0.706 / Num. unique obs: 1261

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HSJ

1hsj


Resolution: 2.303→32.209 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2288 1995 7.87 %
Rwork0.1726 --
obs0.1771 25341 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.303→32.209 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3887 0 23 300 4210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084006
X-RAY DIFFRACTIONf_angle_d1.1175433
X-RAY DIFFRACTIONf_dihedral_angle_d13.0331479
X-RAY DIFFRACTIONf_chiral_restr0.044597
X-RAY DIFFRACTIONf_plane_restr0.005690
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.303-2.36060.32781360.23891617X-RAY DIFFRACTION98
2.3606-2.42440.27751440.20911635X-RAY DIFFRACTION100
2.4244-2.49570.23521320.2111680X-RAY DIFFRACTION100
2.4957-2.57630.26781390.20731641X-RAY DIFFRACTION100
2.5763-2.66830.24641350.18871647X-RAY DIFFRACTION100
2.6683-2.77510.25561460.19291677X-RAY DIFFRACTION100
2.7751-2.90130.23891350.19211632X-RAY DIFFRACTION100
2.9013-3.05410.26331490.2011681X-RAY DIFFRACTION100
3.0541-3.24530.27371440.19081687X-RAY DIFFRACTION100
3.2453-3.49560.22761450.18391661X-RAY DIFFRACTION100
3.4956-3.84690.21471450.15471662X-RAY DIFFRACTION100
3.8469-4.40230.21621460.14541680X-RAY DIFFRACTION100
4.4023-5.54190.17361420.13691699X-RAY DIFFRACTION100
5.5419-32.2090.20471570.15631747X-RAY DIFFRACTION99

+
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