[English] 日本語
Yorodumi
- PDB-6xdj: Crystal Structure Analysis of MBP-SIN3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6xdj
TitleCrystal Structure Analysis of MBP-SIN3
ComponentsMaltodextrin-binding protein,Transcriptional regulatory protein SIN3
KeywordsTRANSCRIPTION / RPD3 histone deacetylase complexes / epigenetic repression
Function / homology
Function and homology information


negative regulation of silent mating-type cassette heterochromatin formation / Rpd3L complex / negative regulation of rDNA heterochromatin formation / Rpd3L-Expanded complex / Rpd3S complex / rDNA chromatin condensation / nucleophagy / cell envelope / regulation of DNA-templated DNA replication initiation / negative regulation of transcription by RNA polymerase I ...negative regulation of silent mating-type cassette heterochromatin formation / Rpd3L complex / negative regulation of rDNA heterochromatin formation / Rpd3L-Expanded complex / Rpd3S complex / rDNA chromatin condensation / nucleophagy / cell envelope / regulation of DNA-templated DNA replication initiation / negative regulation of transcription by RNA polymerase I / Sin3-type complex / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / meiotic cell cycle / double-strand break repair via nonhomologous end joining / G2/M transition of mitotic cell cycle / transcription corepressor activity / nucleosome assembly / cellular response to heat / transcription coactivator activity / periplasmic space / cell division / regulation of transcription by RNA polymerase II / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / metal ion binding / identical protein binding / nucleus
Similarity search - Function
Paired amphipathic helix / Paired amphipathic helix 2 (pah2 repeat) / Histone deacetylase interacting domain / Sin3, C-terminal / Transcriptional regulatory protein Sin3-like / Sin3 family co-repressor / C-terminal domain of Sin3a protein / Histone deacetylase (HDAC) interacting / Paired amphipathic helix / Paired amphipathic helix superfamily ...Paired amphipathic helix / Paired amphipathic helix 2 (pah2 repeat) / Histone deacetylase interacting domain / Sin3, C-terminal / Transcriptional regulatory protein Sin3-like / Sin3 family co-repressor / C-terminal domain of Sin3a protein / Histone deacetylase (HDAC) interacting / Paired amphipathic helix / Paired amphipathic helix superfamily / Paired amphipathic helix repeat / PAH domain profile. / 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 / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
alpha-maltose / beta-maltotriose / Maltodextrin-binding protein / Transcriptional regulatory protein SIN3
Similarity search - Component
Biological speciesSerratia sp. (bacteria)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsSeo, H.-S. / Dhe-Paganon, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: To be published
Title: Crystal Structure Analysis of MBP-SIN3
Authors: Seo, H.-S.
History
DepositionJun 10, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Maltodextrin-binding protein,Transcriptional regulatory protein SIN3
B: Maltodextrin-binding protein,Transcriptional regulatory protein SIN3
C: Maltodextrin-binding protein,Transcriptional regulatory protein SIN3
D: Maltodextrin-binding protein,Transcriptional regulatory protein SIN3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,4578
Polymers195,6014
Non-polymers1,8564
Water12,647702
1
A: Maltodextrin-binding protein,Transcriptional regulatory protein SIN3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4052
Polymers48,9001
Non-polymers5041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Maltodextrin-binding protein,Transcriptional regulatory protein SIN3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2432
Polymers48,9001
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Maltodextrin-binding protein,Transcriptional regulatory protein SIN3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4052
Polymers48,9001
Non-polymers5041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Maltodextrin-binding protein,Transcriptional regulatory protein SIN3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4052
Polymers48,9001
Non-polymers5041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.730, 144.860, 97.090
Angle α, β, γ (deg.)90.000, 107.970, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Maltodextrin-binding protein,Transcriptional regulatory protein SIN3


Mass: 48900.305 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia sp. (strain FS14) (bacteria), (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: malE, SIN3 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4P1LXE0, UniProt: P22579
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-maltotriose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 504.438 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-maltotriose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5][a2122h-1a_1-5]/1-2-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 702 / 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: 2.73 Å3/Da / Density % sol: 54.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M Bis-Tris, pH 6.0, 1.6M Ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.2→75.841 Å / Num. obs: 105169 / % possible obs: 99.1 % / Redundancy: 3.5 % / Biso Wilson estimate: 39.692 Å2 / Rpim(I) all: 0.062 / Rrim(I) all: 0.117 / Net I/σ(I): 7.8
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.4 %

Resolution (Å)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all% possible all
2.2-2.2411775052240.7341.37199
5.97-75.8922.81819153450.0230.04398.7

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XDSdata reduction
xia2data scaling
PHASERphasing
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JBZ

4jbz


Resolution: 2.2→75.841 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2399 5335 5.08 %
Rwork0.2057 99773 -
obs0.2074 105108 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.71 Å2 / Biso mean: 51.6779 Å2 / Biso min: 30.94 Å2
Refinement stepCycle: final / Resolution: 2.2→75.841 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12508 0 125 702 13335
Biso mean--43.38 52.26 -
Num. residues----1636
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00312944
X-RAY DIFFRACTIONf_angle_d0.58217625
X-RAY DIFFRACTIONf_dihedral_angle_d2.7017710
X-RAY DIFFRACTIONf_chiral_restr0.0421977
X-RAY DIFFRACTIONf_plane_restr0.0032261
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2-2.2250.35311900.3342326299
2.225-2.25120.35481750.317326599
2.2512-2.27870.36191690.3067330297
2.2787-2.30750.31181790.2962315796
2.3075-2.33790.33491780.2894334399
2.3379-2.36990.33731750.28193314100
2.3699-2.40380.33171880.279326299
2.4038-2.43960.33761660.2742336999
2.4396-2.47780.29711730.2621333999
2.4778-2.51840.33511710.2606327899
2.5184-2.56180.29251930.255337799
2.5618-2.60840.29891730.2552330499
2.6084-2.65860.31031880.25173366100
2.6586-2.71280.26771710.2492330699
2.7128-2.77180.3021720.24343354100
2.7718-2.83630.30551650.2315336399
2.8363-2.90720.26361760.23373319100
2.9072-2.98590.24011830.22233327100
2.9859-3.07370.28171840.22033343100
3.0737-3.17290.24341920.22243319100
3.1729-3.28630.25861580.2185334999
3.2863-3.41790.27481750.2132328798
3.4179-3.57350.24011780.19893353100
3.5735-3.76190.2341740.1873377100
3.7619-3.99750.21451950.17673352100
3.9975-4.30620.19481790.16473315100
4.3062-4.73950.17551710.14973391100
4.7395-5.42510.17451770.15823379100
5.4251-6.83440.20541800.1876331198
6.8344-75.8410.19971870.1883339099
Refinement TLS params.Method: refined / Origin x: 39.6121 Å / Origin y: 100.595 Å / Origin z: 115.2588 Å
111213212223313233
T0.4248 Å20.0146 Å2-0.0418 Å2-0.3823 Å20.039 Å2--0.3918 Å2
L0.237 °20.0077 °2-0.093 °2-0.243 °20.0981 °2--0.3427 °2
S0.0222 Å °0.0203 Å °0.0095 Å °-0.0665 Å °-0.0297 Å °0.0162 Å °-0.0411 Å °0.0053 Å °0.0111 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 442
2X-RAY DIFFRACTION1allB1 - 443
3X-RAY DIFFRACTION1allC4 - 389
4X-RAY DIFFRACTION1allD1 - 501
5X-RAY DIFFRACTION1allC501
6X-RAY DIFFRACTION1allA501
7X-RAY DIFFRACTION1allB501
8X-RAY DIFFRACTION1allS1 - 702

+
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