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- PDB-5f0n: Cohesin subunit Pds5 -

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Basic information

Entry
Database: PDB / ID: 5f0n
TitleCohesin subunit Pds5
Componentscohesin subunit Pds5,cohesin subunit Pds5, cohesin subunit Pds5,KLTH0D07062p,cohesin subunit Pds5,cohesin subunit Pds5, cohesin subunit Pds5,KLTH0D07062p,cohesin subunit Pds5,cohesin subunit Pds5, cohesin subunit Pds5,KLTH0D07062p,cohesin subunit Pds5,cohesin subunit Pds5, cohesin subunit Pds5
KeywordsCELL CYCLE / heat repeat cohesin subunit
Function / homology
Function and homology information


mitotic sister chromatid cohesion / cell division / DNA repair / chromatin / nucleus
Similarity search - Function
Sister chromatid cohesion protein Pds5 / Sister chromatid cohesion protein PDS5 protein / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Biological speciesLachancea thermotolerans (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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 20, 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 / diffrn_radiation_wavelength / pdbx_entry_details
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: cohesin subunit Pds5,cohesin subunit Pds5, cohesin subunit Pds5,KLTH0D07062p,cohesin subunit Pds5,cohesin subunit Pds5, cohesin subunit Pds5,KLTH0D07062p,cohesin subunit Pds5,cohesin subunit Pds5, cohesin subunit Pds5,KLTH0D07062p,cohesin subunit Pds5,cohesin subunit Pds5, cohesin subunit Pds5


Theoretical massNumber of molelcules
Total (without water)129,6801
Polymers129,6801
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area49470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)238.210, 238.210, 80.660
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,cohesin subunit Pds5, cohesin subunit Pds5,KLTH0D07062p,cohesin subunit Pds5,cohesin subunit Pds5, cohesin subunit Pds5,KLTH0D07062p,cohesin subunit Pds5,cohesin subunit Pds5, cohesin subunit Pds5,KLTH0D07062p,cohesin subunit Pds5,cohesin subunit Pds5, cohesin subunit Pds5


Mass: 129680.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lachancea thermotolerans (fungus), (gene. exp.) Lachancea thermotolerans (strain ATCC 56472 / CBS 6340 / NRRL Y-8284) (fungus)
Gene: 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
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: 3.76 Å3/Da / Density % sol: 67.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM HEPES pH 7.5, and 1.3-1.6 M lithium sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9796 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 3.2→46.67 Å / Num. obs: 28140 / % possible obs: 100 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.109 / Rsym value: 0.056 / Net I/σ(I): 14.5

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→46.667 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 2.83 / Phase error: 33.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2951 1385 5.3 %Random selection
Rwork0.236 24730 --
obs0.2392 26115 92.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 161.27 Å2 / Biso mean: 65.4874 Å2 / Biso min: 17.76 Å2
Refinement stepCycle: final / Resolution: 3.2→46.667 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8213 0 0 0 8213
Num. residues----1038
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038366
X-RAY DIFFRACTIONf_angle_d0.72611318
X-RAY DIFFRACTIONf_chiral_restr0.0411316
X-RAY DIFFRACTIONf_plane_restr0.0051429
X-RAY DIFFRACTIONf_dihedral_angle_d17.6194995
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2002-3.31450.3801860.32051195128146
3.3145-3.44720.33721330.30292190232383
3.4472-3.6040.39811440.297826762820100
3.604-3.79390.32961370.2626852822100
3.7939-4.03150.271660.235226262792100
4.0315-4.34260.31041450.213726812826100
4.3426-4.77920.26211290.195826812810100
4.7792-5.46980.25641460.218626752821100
5.4698-6.88790.28231420.268226602802100
6.8879-46.67240.27591570.211526612818100

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