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- PDB-7vrc: Structure of the Yeast SNF11/SNF2 complex -

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Basic information

Entry
Database: PDB / ID: 7vrc
TitleStructure of the Yeast SNF11/SNF2 complex
Components
  • Transcription regulatory protein SNF11
  • XXYS1_4_G0032080.mRNA.1.CDS.1
KeywordsNUCLEAR PROTEIN / helix bundle
Function / homologySWI/SNF complex / chromatin remodeling / chromatin / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus / cytosol / : / Transcription regulatory protein SNF11
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.147 Å
AuthorsCheng, Y. / Chen, F. / Zhou, H. / Long, J.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870750 China
National Natural Science Foundation of China (NSFC)31670758 China
CitationJournal: To Be Published
Title: Structure of the Yeast SNF11/SNF2 complex
Authors: Cheng, Y. / Chen, F. / Zhou, H. / Long, J.
History
DepositionOct 22, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcription regulatory protein SNF11
B: XXYS1_4_G0032080.mRNA.1.CDS.1
C: Transcription regulatory protein SNF11
D: XXYS1_4_G0032080.mRNA.1.CDS.1


Theoretical massNumber of molelcules
Total (without water)51,6084
Polymers51,6084
Non-polymers00
Water2,522140
1
A: Transcription regulatory protein SNF11
B: XXYS1_4_G0032080.mRNA.1.CDS.1


Theoretical massNumber of molelcules
Total (without water)25,8042
Polymers25,8042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-21 kcal/mol
Surface area9720 Å2
MethodPISA
2
C: Transcription regulatory protein SNF11
D: XXYS1_4_G0032080.mRNA.1.CDS.1


Theoretical massNumber of molelcules
Total (without water)25,8042
Polymers25,8042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-21 kcal/mol
Surface area9530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.445, 63.539, 118.466
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Transcription regulatory protein SNF11 / SWI/SNF complex component SNF11


Mass: 18678.834 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: SNF11, YDR073W, D4411 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P38956
#2: Protein XXYS1_4_G0032080.mRNA.1.CDS.1 / SNF2


Mass: 7125.299 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PACBIOSEQ_LOCUS5717 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A7I9GI57
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O

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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: 1.73 Å3/Da / Density % sol: 28.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.79 M sodium phosphate monobasic monohydrate and 0.61 M potassium phosphate dibasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.147→50 Å / Num. obs: 20093 / % possible obs: 99.7 % / Redundancy: 4.8 % / Rpim(I) all: 0.052 / Net I/σ(I): 14.78
Reflection shellResolution: 2.147→2.19 Å / Num. unique obs: 959 / Rpim(I) all: 0.391

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10_2155refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.147→44.044 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2599 959 5.08 %
Rwork0.1942 17909 -
obs0.1974 18868 93.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 68.43 Å2 / Biso mean: 29.4193 Å2 / Biso min: 9.2 Å2
Refinement stepCycle: final / Resolution: 2.147→44.044 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2564 0 0 140 2704
Biso mean---37.78 -
Num. residues----316
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082602
X-RAY DIFFRACTIONf_angle_d0.9323523
X-RAY DIFFRACTIONf_chiral_restr0.055422
X-RAY DIFFRACTIONf_plane_restr0.006453
X-RAY DIFFRACTIONf_dihedral_angle_d14.91637
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.147-2.26020.27111010.203187669
2.2602-2.40180.27911130.1959232687
2.4018-2.58720.25721430.1958264498
2.5872-2.84760.22871620.18912706100
2.8476-3.25950.26491150.19532746100
3.2595-4.10610.26381600.17812761100
4.1061-5.830.26271650.2064285098

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