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- PDB-4uvk: Cohesin subunit Scc3 from Z. rouxii, 88-1035 -

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Basic information

Entry
Database: PDB / ID: 4uvk
TitleCohesin subunit Scc3 from Z. rouxii, 88-1035
ComponentsZYRO0D15994P
KeywordsCELL CYCLE / COHESIN / MITOSIS / HEAT REPEATS / SMC PROTEINS
Function / homology
Function and homology information


: / Cohesin subunit SCC3, C-terminal domain / STAG / Stromalin conservative domain / Cohesin subunit Scc3/SA / STAG domain / Stromalin conservative domain / Stromalin conservative (SCD) domain profile. / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Biological speciesZYGOSACCHAROMYCES ROUXII (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsRoig, M.B. / Nasmyth, K. / Lowe, J.
CitationJournal: FEBS Lett. / Year: 2014
Title: Structure and Function of Cohesins Scc3/Sa Regulatory Subunit
Authors: Roig, M.B. / Lowe, J. / Chan, K.L. / Beckouet, F. / Metson, J. / Nasmyth, K.
History
DepositionAug 6, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 20, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2014Group: Database references
Revision 1.2Oct 8, 2014Group: Database references
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ZYRO0D15994P


Theoretical massNumber of molelcules
Total (without water)109,7491
Polymers109,7491
Non-polymers00
Water3,765209
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.372, 109.176, 159.029
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ZYRO0D15994P / SCC3


Mass: 109749.078 Da / Num. of mol.: 1 / Fragment: SCC3 HIS-TAGGED, UNP RESIDUES 88-1035
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ZYGOSACCHAROMYCES ROUXII (yeast) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: C5DWM3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 65 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.0332
DetectorType: DECTRIS PILATUS / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 39907 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 52 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.3
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.5 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.6→48.347 Å / SU ML: 0.35 / σ(F): 1 / Phase error: 24.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.245 3748 5 %
Rwork0.1871 --
obs0.1901 37521 98.85 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.01 Å2 / ksol: 0.348 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.0655 Å20 Å2-0 Å2
2--2.729 Å2-0 Å2
3----2.6635 Å2
Refinement stepCycle: LAST / Resolution: 2.6→48.347 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7101 0 0 209 7310
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0157235
X-RAY DIFFRACTIONf_angle_d1.5499769
X-RAY DIFFRACTIONf_dihedral_angle_d18.2432684
X-RAY DIFFRACTIONf_chiral_restr0.0781136
X-RAY DIFFRACTIONf_plane_restr0.0061221
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.63290.33791260.27322701X-RAY DIFFRACTION99
2.6329-2.66760.31711200.25652624X-RAY DIFFRACTION99
2.6676-2.70410.29291400.24642668X-RAY DIFFRACTION99
2.7041-2.74280.33231520.24182652X-RAY DIFFRACTION99
2.7428-2.78370.32971390.25252642X-RAY DIFFRACTION99
2.7837-2.82720.29681340.23472638X-RAY DIFFRACTION99
2.8272-2.87350.28661370.23322652X-RAY DIFFRACTION99
2.8735-2.92310.33581760.22422643X-RAY DIFFRACTION99
2.9231-2.97620.24231550.20712576X-RAY DIFFRACTION99
2.9762-3.03350.27251120.19772683X-RAY DIFFRACTION99
3.0335-3.09540.32621110.212666X-RAY DIFFRACTION99
3.0954-3.16270.26111410.20642634X-RAY DIFFRACTION99
3.1627-3.23620.24451370.18382642X-RAY DIFFRACTION99
3.2362-3.31710.24621680.18522659X-RAY DIFFRACTION99
3.3171-3.40680.29931330.19552625X-RAY DIFFRACTION99
3.4068-3.5070.27491290.20682665X-RAY DIFFRACTION99
3.507-3.62020.27341480.18422637X-RAY DIFFRACTION99
3.6202-3.74950.28281410.1832632X-RAY DIFFRACTION99
3.7495-3.89960.21311240.18142671X-RAY DIFFRACTION99
3.8996-4.0770.22851300.16052644X-RAY DIFFRACTION99
4.077-4.29180.20761540.13782605X-RAY DIFFRACTION99
4.2918-4.56050.18331450.13452630X-RAY DIFFRACTION99
4.5605-4.91230.18381610.13522630X-RAY DIFFRACTION99
4.9123-5.40610.20861210.17162634X-RAY DIFFRACTION99
5.4061-6.1870.26971310.21742633X-RAY DIFFRACTION98
6.187-7.78960.21031480.20782604X-RAY DIFFRACTION98
7.7896-48.35560.19491350.16732604X-RAY DIFFRACTION97

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