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- PDB-7e29: Crystal Structure of Saccharomyces cerevisiae Ioc4 PWWP domain fu... -

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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 / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport ...Isw1b complex / Isw1 complex / sister chromatid cohesion / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / 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 / nucleus / membrane
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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

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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: 2.3 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

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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

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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

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