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- PDB-6xdj: Crystal Structure Analysis of MBP-SIN3 -

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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 / Rpd3S complex / Rpd3L-Expanded complex / negative regulation of rDNA heterochromatin formation / rDNA chromatin condensation / nucleophagy / regulation of DNA-templated DNA replication initiation / negative regulation of transcription by RNA polymerase I / Sin3-type complex ...negative regulation of silent mating-type cassette heterochromatin formation / Rpd3L complex / Rpd3S complex / Rpd3L-Expanded complex / negative regulation of rDNA heterochromatin formation / rDNA chromatin condensation / nucleophagy / regulation of DNA-templated DNA replication initiation / negative regulation of transcription by RNA polymerase I / Sin3-type complex / carbohydrate transmembrane transporter activity / nucleosome assembly / double-strand break repair via nonhomologous end joining / transcription corepressor activity / transcription coactivator activity / periplasmic space / cell cycle / cell division / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus
Similarity search - Function
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. ...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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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 / Water


Mass: 18.015 Da / Num. of mol.: 702 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

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

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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

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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

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Phasing

PhasingMethod: molecular replacement

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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

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