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- PDB-5msn: Structure of the Dcc1 Protein -

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Basic information

Entry
Database: PDB / ID: 5msn
TitleStructure of the Dcc1 Protein
ComponentsDCC1 protein
KeywordsCELL CYCLE / winged-helix / DNA repair
Function / homology
Function and homology information


maintenance of mitotic sister chromatid cohesion / Ctf18 RFC-like complex / maintenance of DNA trinucleotide repeats / mitotic sister chromatid cohesion / chromosome, centromeric region / DNA replication / chromatin
Similarity search - Function
Sister chromatid cohesion protein Dcc1 / Sister chromatid cohesion protein Dcc1
Similarity search - Domain/homology
Sister chromatid cohesion protein DCC1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.002 Å
AuthorsWade, B.O. / Singleton, M.R.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Cancer Research UKFC0010155 United Kingdom
Wellcome TrustFC0010155 United Kingdom
Medical Research Council (United Kingdom)FC0010155 United Kingdom
CitationJournal: EMBO Rep. / Year: 2017
Title: Structural studies of RFC(C)(tf18) reveal a novel chromatin recruitment role for Dcc1.
Authors: Wade, B.O. / Liu, H.W. / Samora, C.P. / Uhlmann, F. / Singleton, M.R.
History
DepositionJan 5, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2017Group: Database references
Revision 1.2Apr 12, 2017Group: Database references
Revision 2.0Sep 13, 2017Group: Atomic model / Author supporting evidence / Category: atom_site / pdbx_audit_support
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization
Revision 2.1May 8, 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: DCC1 protein
B: DCC1 protein
C: DCC1 protein
D: DCC1 protein


Theoretical massNumber of molelcules
Total (without water)135,1644
Polymers135,1644
Non-polymers00
Water10,323573
1
A: DCC1 protein


Theoretical massNumber of molelcules
Total (without water)33,7911
Polymers33,7911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DCC1 protein


Theoretical massNumber of molelcules
Total (without water)33,7911
Polymers33,7911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: DCC1 protein


Theoretical massNumber of molelcules
Total (without water)33,7911
Polymers33,7911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: DCC1 protein


Theoretical massNumber of molelcules
Total (without water)33,7911
Polymers33,7911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.682, 100.697, 83.495
Angle α, β, γ (deg.)90.00, 100.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
DCC1 protein / Defective in sister chromatid cohesion protein 1


Mass: 33790.910 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Gene: DCC1, YCL016C, YCL16C / Production host: Escherichia coli (E. coli) / References: UniProt: P25559
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 573 / Source method: isolated from a natural source / Formula: H2O

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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: 2.1 Å3/Da / Density % sol: 41.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M potassium sodium tartrate and 18% PEG 3,350

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 31, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2→29.36 Å / Num. obs: 71317 / % possible obs: 95 % / Redundancy: 4 % / Rmerge(I) obs: 0.1158 / Net I/σ(I): 8.43
Reflection shellResolution: 2.002→2.074 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.9735 / Mean I/σ(I) obs: 1.31 / Num. measured obs: 6489 / % possible all: 87

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
xia2data reduction
Aimlessdata scaling
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.002→29.357 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2301 3560 4.99 %
Rwork0.1892 --
obs0.1912 71313 94.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.002→29.357 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8358 0 0 573 8931
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0138545
X-RAY DIFFRACTIONf_angle_d1.59211526
X-RAY DIFFRACTIONf_dihedral_angle_d10.9395174
X-RAY DIFFRACTIONf_chiral_restr0.091272
X-RAY DIFFRACTIONf_plane_restr0.011454
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0024-2.02980.3546910.30412088X-RAY DIFFRACTION72
2.0298-2.05880.32071560.28072686X-RAY DIFFRACTION96
2.0588-2.08950.31991470.27722744X-RAY DIFFRACTION96
2.0895-2.12210.29381530.2632692X-RAY DIFFRACTION96
2.1221-2.15690.28961440.25482752X-RAY DIFFRACTION96
2.1569-2.19410.31381300.24812702X-RAY DIFFRACTION95
2.1941-2.2340.28631220.24282484X-RAY DIFFRACTION87
2.234-2.27690.28931480.23632505X-RAY DIFFRACTION89
2.2769-2.32340.29431580.22172791X-RAY DIFFRACTION98
2.3234-2.37390.27471670.21692797X-RAY DIFFRACTION98
2.3739-2.42910.25641590.21332762X-RAY DIFFRACTION98
2.4291-2.48980.2731580.21242775X-RAY DIFFRACTION98
2.4898-2.55710.25261380.2072813X-RAY DIFFRACTION98
2.5571-2.63230.24651520.19782795X-RAY DIFFRACTION98
2.6323-2.71720.24171390.19472814X-RAY DIFFRACTION98
2.7172-2.81420.26121380.1862777X-RAY DIFFRACTION98
2.8142-2.92680.22851280.18092819X-RAY DIFFRACTION98
2.9268-3.05990.23881410.17822770X-RAY DIFFRACTION97
3.0599-3.2210.19921450.1782513X-RAY DIFFRACTION89
3.221-3.42260.21361480.16612650X-RAY DIFFRACTION92
3.4226-3.68630.20521380.1622845X-RAY DIFFRACTION99
3.6863-4.05650.17261360.15552851X-RAY DIFFRACTION99
4.0565-4.64140.19721350.14852842X-RAY DIFFRACTION98
4.6414-5.84020.1841410.17162756X-RAY DIFFRACTION96
5.8402-29.36030.21611480.19372730X-RAY DIFFRACTION93

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