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- PDB-5frr: Structure of the Pds5-Scc1 complex and implications for cohesin f... -

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Basic information

Entry
Database: PDB / ID: 5frr
TitleStructure of the Pds5-Scc1 complex and implications for cohesin function
ComponentsSISTER CHROMATID COHESION PROTEIN PDS5
KeywordsCELL CYCLE
Function / homology
Function and homology information


meiotic recombination initiation complex / Establishment of Sister Chromatid Cohesion / Resolution of Sister Chromatid Cohesion / meiotic DNA double-strand break formation / homologous chromosome pairing at meiosis / chromatin looping / mitotic chromosome condensation / mitotic sister chromatid cohesion / meiotic cell cycle / condensed nuclear chromosome ...meiotic recombination initiation complex / Establishment of Sister Chromatid Cohesion / Resolution of Sister Chromatid Cohesion / meiotic DNA double-strand break formation / homologous chromosome pairing at meiosis / chromatin looping / mitotic chromosome condensation / mitotic sister chromatid cohesion / meiotic cell cycle / condensed nuclear chromosome / double-strand break repair / cell division / chromatin / structural molecule activity / nucleus / cytosol
Similarity search - Function
Sister chromatid cohesion protein Pds5 / non-SMC mitotic condensation complex subunit 1 / Sister chromatid cohesion protein PDS5 protein / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Sister chromatid cohesion protein PDS5
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 5.8 Å
AuthorsMuir, K.W. / Kschonsak, M. / Li, Y. / Metz, J. / Haering, C.H. / Panne, D.
CitationJournal: Cell Rep. / Year: 2016
Title: Structure of the Pds5-Scc1 Complex and Implications for Cohesin Function
Authors: Muir, K.W. / Kschonsak, M. / Li, Y. / Metz, J. / Haering, C.H. / Panne, D.
History
DepositionDec 22, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Database references
Revision 1.2Mar 23, 2016Group: Database references
Revision 1.3Apr 27, 2016Group: Data collection
Revision 1.4Aug 23, 2017Group: Data collection / Category: diffrn_detector / diffrn_source
Item: _diffrn_detector.type / _diffrn_source.pdbx_wavelength / _diffrn_source.pdbx_wavelength_list
Revision 1.5May 3, 2023Group: Data collection / Database references / Other
Category: database_2 / diffrn_radiation_wavelength / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SISTER CHROMATID COHESION PROTEIN PDS5
B: SISTER CHROMATID COHESION PROTEIN PDS5


Theoretical massNumber of molelcules
Total (without water)161,4762
Polymers161,4762
Non-polymers00
Water0
1
A: SISTER CHROMATID COHESION PROTEIN PDS5


Theoretical massNumber of molelcules
Total (without water)80,7381
Polymers80,7381
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SISTER CHROMATID COHESION PROTEIN PDS5


Theoretical massNumber of molelcules
Total (without water)80,7381
Polymers80,7381
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)283.690, 283.690, 172.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein SISTER CHROMATID COHESION PROTEIN PDS5 / PRECOCIOUS DISSOCIATION OF SISTERS PROTEIN 5 / PDS5


Mass: 80738.062 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q04264

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.95 Å3/Da / Density % sol: 58.33 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 5.8→50 Å / Num. obs: 10082 / % possible obs: 99.3 % / Observed criterion σ(I): 1.5 / Redundancy: 7.6 % / Rmerge(I) obs: 0.02 / Net I/σ(I): 17.1
Reflection shellHighest resolution: 5.8 Å / Mean I/σ(I) obs: 1.57

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Processing

Software
NameClassification
CNSrefinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 5.8→50 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.3111 518 4.9 %RANDOM
Rwork0.249 ---
obs0.249 10081 95 %-
Solvent computationBsol: 375.032 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 424 Å2
Refinement stepCycle: LAST / Resolution: 5.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10858 0 0 0 10858
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.002749
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg0.59318
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1AA
X-RAY DIFFRACTION2AA
X-RAY DIFFRACTION3AA
X-RAY DIFFRACTION4AA
X-RAY DIFFRACTION5AA

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