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- PDB-5f0o: Cohesin subunit Pds5 in complex with Scc1 -

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Basic information

Entry
Database: PDB / ID: 5f0o
TitleCohesin subunit Pds5 in complex with Scc1
Components
  • KLTH0G16610p
  • cohesin subunit Pds5, KLTH0D07062p,KLTH0D07062p,KLTH0D07062p,cohesin subunit Pds5, KLTH0D07062p,KLTH0D07062p,KLTH0D07062p,cohesin subunit Pds5, KLTH0D07062p,KLTH0D07062p,KLTH0D07062p,cohesin subunit Pds5, KLTH0D07062p,KLTH0D07062p
KeywordsCELL CYCLE / heat repeat cohesin subunit
Function / homology
Function and homology information


mitotic cohesin complex / replication-born double-strand break repair via sister chromatid exchange / mitotic sister chromatid cohesion / cell division / DNA repair / chromatin binding / chromatin / nucleus
Similarity search - Function
Sister chromatid cohesion protein Pds5 / Sister chromatid cohesion protein PDS5 protein / Rad21/Rec8-like protein, C-terminal, eukaryotic / Rad21/Rec8-like protein, N-terminal / Rad21/Rec8-like protein / Conserved region of Rad21 / Rec8 like protein / N terminus of Rad21 / Rec8 like protein / ScpA-like, C-terminal / Armadillo-like helical / Armadillo-type fold / Winged helix DNA-binding domain superfamily
Similarity search - Domain/homology
KLTH0D07062p / KLTH0G16610p
Similarity search - Component
Biological speciesLachancea thermotolerans (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsLee, B.-G. / Jansma, M. / Nasmyth, K. / Lowe, J.
CitationJournal: Cell Rep / Year: 2016
Title: Crystal Structure of the Cohesin Gatekeeper Pds5 and in Complex with Kleisin Scc1.
Authors: Lee, B.G. / Roig, M.B. / Jansma, M. / Petela, N. / Metson, J. / Nasmyth, K. / Lowe, J.
History
DepositionNov 27, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details
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: cohesin subunit Pds5, KLTH0D07062p,KLTH0D07062p,KLTH0D07062p,cohesin subunit Pds5, KLTH0D07062p,KLTH0D07062p,KLTH0D07062p,cohesin subunit Pds5, KLTH0D07062p,KLTH0D07062p,KLTH0D07062p,cohesin subunit Pds5, KLTH0D07062p,KLTH0D07062p
E: KLTH0G16610p


Theoretical massNumber of molelcules
Total (without water)128,4732
Polymers128,4732
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-11 kcal/mol
Surface area48510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)235.400, 235.400, 94.290
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein cohesin subunit Pds5, KLTH0D07062p,KLTH0D07062p,KLTH0D07062p,cohesin subunit Pds5, KLTH0D07062p,KLTH0D07062p,KLTH0D07062p,cohesin subunit Pds5, KLTH0D07062p,KLTH0D07062p,KLTH0D07062p,cohesin subunit Pds5, KLTH0D07062p,KLTH0D07062p


Mass: 125973.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The UNK residues are part of chain A, but we could not correct the exact residues due to low resolution map
Source: (gene. exp.) Lachancea thermotolerans (fungus) / Gene: KLTH0D07062g,Pds5, KLTH0D07062g / Plasmid: pHis17 / Strain: ATCC 56472 / CBS 6340 / NRRL Y-8284 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: C5DGP8
#2: Protein/peptide KLTH0G16610p


Mass: 2499.833 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Lachancea thermotolerans (strain ATCC 56472 / CBS 6340 / NRRL Y-8284) (fungus)
References: UniProt: C5DNF8
Has protein modificationN

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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: 4.31 Å3/Da / Density % sol: 71.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 50 mM sodium cacodylate pH 6.5, 1.4 - 1.6 M ammonium sulphate and 5 mM magnesium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97942 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 3.5→48.49 Å / Num. obs: 22568 / % possible obs: 99.9 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.079 / Rsym value: 0.06 / Net I/σ(I): 11.2

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→44.486 Å / SU ML: 0.56 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 39.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2907 915 4.78 %Random selection
Rwork0.2321 18239 --
obs0.235 19154 78.08 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 188.21 Å2 / Biso mean: 122.8637 Å2 / Biso min: 57.96 Å2
Refinement stepCycle: final / Resolution: 3.5→44.486 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8183 0 0 0 8183
Num. residues----1035
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058329
X-RAY DIFFRACTIONf_angle_d0.83711264
X-RAY DIFFRACTIONf_chiral_restr0.0431319
X-RAY DIFFRACTIONf_plane_restr0.0051416
X-RAY DIFFRACTIONf_dihedral_angle_d18.0584969
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5005-3.6850.3547530.2783992104530
3.685-3.91570.3209950.28411711180651
3.9157-4.21780.3481130.26582419253273
4.2178-4.64190.3331400.24423122326293
4.6419-5.31260.27631710.237233293500100
5.3126-6.68970.38681820.27633343516100
6.6897-44.490.23071610.194433323493100

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