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- PDB-7k7v: The X-ray crystal structure of SSR4, an S. pombe chromatin remode... -

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Basic information

Entry
Database: PDB / ID: 7k7v
TitleThe X-ray crystal structure of SSR4, an S. pombe chromatin remodelling protein: iodide derivative
ComponentsSWI/SNF and RSC complexes subunit ssr4
KeywordsGENE REGULATION / chromatin remodelling / SAD phasing / novel structure
Function / homology
Function and homology information


RSC-type complex / SWI/SNF complex / transcription initiation-coupled chromatin remodeling / chromatin remodeling / regulation of transcription by RNA polymerase II / chromatin / nucleus / cytosol
Similarity search - Function
SWI/SNF and RSC complexes subunit Ssr4, N-terminal / SWI/SNF and RSC complexes subunit Ssr4, C-terminal / SWI/SNF and RSC complexes subunit Ssr4 N-terminal / SWI/SNF and RSC complexes subunit Ssr4 C-terminal
Similarity search - Domain/homology
IODIDE ION / SWI/SNF and RSC complexes subunit ssr4
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.882 Å
AuthorsPeat, T.S. / Newman, J.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2020
Title: The X-ray crystal structure of the N-terminal domain of Ssr4, a Schizosaccharomyces pombe chromatin-remodelling protein.
Authors: Newman, J. / Nebl, T. / Van, H. / Peat, T.S.
History
DepositionSep 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SWI/SNF and RSC complexes subunit ssr4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8228
Polymers22,3341
Non-polymers4887
Water1,60389
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint-33 kcal/mol
Surface area10270 Å2
Unit cell
Length a, b, c (Å)50.157, 67.496, 67.534
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 SWI/SNF and RSC complexes subunit ssr4


Mass: 22334.494 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: ssr4, SPBP23A10.05 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9P7Y0
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.56 Å3/Da / Density % sol: 51.94 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop
Details: Crystallisation experiments were set up in SD2 sitting drop plates at 8 C with 200 nL protein plus 200 nL reservoir with 50 uL of reservoir in the wells. The protein concentration was 5 ...Details: Crystallisation experiments were set up in SD2 sitting drop plates at 8 C with 200 nL protein plus 200 nL reservoir with 50 uL of reservoir in the wells. The protein concentration was 5 mg/mL. Reservoir conditions contained 1.5 to 1.9 M ammonium sulfate, 0.7-12% dioxane and either 100 mM MES, 100 mM bis-tris or 10% (v/v) malate-MES-tris buffer at a pH between 5.5 and 5.8
PH range: 5.5 - 5.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1.5483 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5483 Å / Relative weight: 1
ReflectionResolution: 1.88→40.3 Å / Num. obs: 18912 / % possible obs: 98.3 % / Redundancy: 13 % / CC1/2: 0.997 / Rmerge(I) obs: 0.161 / Rpim(I) all: 0.046 / Net I/σ(I): 13.5
Reflection shellResolution: 1.88→1.92 Å / Redundancy: 8.9 % / Rmerge(I) obs: 1.246 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 976 / CC1/2: 0.488 / Rpim(I) all: 0.432 / % possible all: 78.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: SAD / Resolution: 1.882→40.291 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.668 / SU ML: 0.078 / Cross valid method: FREE R-VALUE / ESU R: 0.124 / ESU R Free: 0.119
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2041 971 5.148 %
Rwork0.168 17889 -
all0.17 --
obs-18860 98.152 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 24.287 Å2
Baniso -1Baniso -2Baniso -3
1--0.377 Å2-0 Å2-0 Å2
2--0.16 Å2-0 Å2
3---0.217 Å2
Refinement stepCycle: LAST / Resolution: 1.882→40.291 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1526 0 12 89 1627
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0131610
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171482
X-RAY DIFFRACTIONr_angle_refined_deg1.6251.6442207
X-RAY DIFFRACTIONr_angle_other_deg1.4281.5653425
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8645197
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.91921.64679
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.22415239
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.257159
X-RAY DIFFRACTIONr_chiral_restr0.0760.2205
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021822
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02376
X-RAY DIFFRACTIONr_nbd_refined0.2060.2259
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1840.21359
X-RAY DIFFRACTIONr_nbtor_refined0.1760.2787
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.2760
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.262
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1980.26
X-RAY DIFFRACTIONr_nbd_other0.1770.244
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1340.28
X-RAY DIFFRACTIONr_mcbond_it2.5662.31782
X-RAY DIFFRACTIONr_mcbond_other2.5632.305781
X-RAY DIFFRACTIONr_mcangle_it3.9373.441981
X-RAY DIFFRACTIONr_mcangle_other3.9363.447982
X-RAY DIFFRACTIONr_scbond_it3.5722.689828
X-RAY DIFFRACTIONr_scbond_other3.5712.688829
X-RAY DIFFRACTIONr_scangle_it5.7093.8681226
X-RAY DIFFRACTIONr_scangle_other5.7063.8681227
X-RAY DIFFRACTIONr_lrange_it7.89843.8296472
X-RAY DIFFRACTIONr_lrange_other7.88743.786433
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.882-1.9310.392620.3651077X-RAY DIFFRACTION80.7229
1.931-1.9840.226840.2011273X-RAY DIFFRACTION100
1.984-2.0410.18500.1611277X-RAY DIFFRACTION99.8495
2.041-2.1040.269760.1671203X-RAY DIFFRACTION100
2.104-2.1720.204630.1641186X-RAY DIFFRACTION100
2.172-2.2490.199650.1561129X-RAY DIFFRACTION100
2.249-2.3330.215550.1581123X-RAY DIFFRACTION99.9152
2.333-2.4280.239620.1551054X-RAY DIFFRACTION100
2.428-2.5360.238610.1571017X-RAY DIFFRACTION99.9073
2.536-2.6590.197560.155988X-RAY DIFFRACTION99.9043
2.659-2.8030.178410.159956X-RAY DIFFRACTION100
2.803-2.9720.224450.159881X-RAY DIFFRACTION99.8921
2.972-3.1760.205460.155854X-RAY DIFFRACTION99.7783
3.176-3.430.154390.153777X-RAY DIFFRACTION99.391
3.43-3.7550.21420.152714X-RAY DIFFRACTION98.9529
3.755-4.1950.2290.151674X-RAY DIFFRACTION98.4594
4.195-4.8380.132380.145564X-RAY DIFFRACTION97.5689
4.838-5.910.179270.191489X-RAY DIFFRACTION98.2857
5.91-8.2950.234200.234412X-RAY DIFFRACTION97.9592
8.295-40.2910.349100.213241X-RAY DIFFRACTION93.3085

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