6XDJ | pdb_00006xdj

Crystal Structure Analysis of MBP-SIN3

PDB DOI: https://doi.org/10.2210/pdb6XDJ/pdb

Classification: TRANSCRIPTION
Organism(s): Serratia sp. FS14, Saccharomyces cerevisiae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-06-10 Released: 2021-06-16
Deposition Author(s): Seo, H.-S., Dhe-Paganon, S.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.240 (Depositor), 0.242 (DCC)
R-Value Work:
0.206 (Depositor), 0.208 (DCC)
R-Value Observed:
0.207 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure Analysis of MBP-SIN3

Seo, H.-S.

To be published.

Macromolecule Content

Total Structure Weight: 197.46 kDa
Atom Count: 13,335
Modeled Residue Count: 1,636
Deposited Residue Count: 1,772
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltodextrin-binding protein,Transcriptional regulatory protein SIN3	A, B, C, D	443	Serratia sp. FS14, Saccharomyces cerevisiae This entity is chimeric	Mutation(s): 0 Gene Names: malE, SIN3
UniProt
Find proteins for P22579 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P22579 Go to UniProtKB: P22579
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P22579
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose	E, G, H	3		N/A	Interactions Focus chain E Focus chain G Focus chain H Interactions & Density Focus chain E Focus chain G Focus chain H
Glycosylation Resources
GlyTouCan: G00395FS GlyCosmos: G00395FS GlyGen: G00395FS

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	F	2		N/A	Interactions Focus chain F Interactions & Density Focus chain F
Glycosylation Resources
GlyTouCan: G07411ON GlyCosmos: G07411ON

Biologically Interesting Molecules (External Reference)

2 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900065 Query on PRD_900065	E, G, H	beta-maltotriose	Oligosaccharide / Nutrient		Interactions Focus chain E Focus chain G Focus chain H Interactions & Density Focus chain E Focus chain G Focus chain H

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001 Query on PRD_900001	F	alpha-maltose	Oligosaccharide / Nutrient		Interactions Focus chain F Interactions & Density Focus chain F

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.240 (Depositor), 0.242 (DCC)
R-Value Work: 0.206 (Depositor), 0.208 (DCC)
R-Value Observed: 0.207 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.73	α = 90
b = 144.86	β = 107.97
c = 97.09	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
xia2	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-06-16

Deposition Author(s):

Dhe-Paganon, S.

Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	--

Revision History (Full details and data files)

Version 1.0: 2021-06-16
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Database references, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.