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- PDB-3oip: Crystal structure of Yeast telomere protein Cdc13 OB1 -

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Basic information

Entry
Database: PDB / ID: 3oip
TitleCrystal structure of Yeast telomere protein Cdc13 OB1
ComponentsCell division control protein 13
KeywordsCELL CYCLE / OB fold / dimer
Function / homology
Function and homology information


CST complex / ribonucleoprotein complex localization / telomerase inhibitor activity / translation elongation factor binding / regulation of telomere maintenance via telomerase / single-stranded telomeric DNA binding / nuclear telomere cap complex / G-rich strand telomeric DNA binding / telomere capping / telomere maintenance via telomerase ...CST complex / ribonucleoprotein complex localization / telomerase inhibitor activity / translation elongation factor binding / regulation of telomere maintenance via telomerase / single-stranded telomeric DNA binding / nuclear telomere cap complex / G-rich strand telomeric DNA binding / telomere capping / telomere maintenance via telomerase / telomere maintenance / chromosome, telomeric region / cell division / identical protein binding
Similarity search - Function
Arc Repressor Mutant, subunit A - #2380 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #800 / Cell division control protein 13, OB2 domain / Cell division control protein 13, OB2 domain / Cell division control protein 13, N-terminal / Cdc13, OB4 dimerization domain / Cell division control protein 13 N-terminus / Cdc13 OB4 dimerization domain / Protection of telomeres protein 1 / Telomeric single stranded DNA binding POT1/Cdc13 ...Arc Repressor Mutant, subunit A - #2380 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #800 / Cell division control protein 13, OB2 domain / Cell division control protein 13, OB2 domain / Cell division control protein 13, N-terminal / Cdc13, OB4 dimerization domain / Cell division control protein 13 N-terminus / Cdc13 OB4 dimerization domain / Protection of telomeres protein 1 / Telomeric single stranded DNA binding POT1/Cdc13 / Telomeric single stranded DNA binding POT1/CDC13 / Telomeric single stranded DNA binding POT1/CDC13 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Arc Repressor Mutant, subunit A / Nucleic acid-binding, OB-fold / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Cell division control protein 13
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.504 Å
AuthorsSun, J. / Yang, Y. / Wan, K. / Mao, N. / Yu, T.Y. / Lin, Y.C. / DeZwaan, D.C. / Freeman, B.C. / Lin, J.J. / Lue, N.F. / Lei, M.
CitationJournal: Cell Res. / Year: 2011
Title: Structural bases of dimerization of yeast telomere protein Cdc13 and its interaction with the catalytic subunit of DNA polymerase alpha.
Authors: Sun, J. / Yang, Y. / Wan, K. / Mao, N. / Yu, T.Y. / Lin, Y.C. / DeZwaan, D.C. / Freeman, B.C. / Lin, J.J. / Lue, N.F. / Lei, M.
History
DepositionAug 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Jul 26, 2023Group: Database references
Category: citation / citation_author ...citation / citation_author / database_2 / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cell division control protein 13


Theoretical massNumber of molelcules
Total (without water)26,6121
Polymers26,6121
Non-polymers00
Water45025
1
A: Cell division control protein 13

A: Cell division control protein 13


Theoretical massNumber of molelcules
Total (without water)53,2252
Polymers53,2252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Buried area2810 Å2
ΔGint-11 kcal/mol
Surface area20350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.515, 68.641, 52.815
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Cell division control protein 13


Mass: 26612.436 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CDC13, YDL220C / Production host: Escherichia coli (E. coli) / References: UniProt: P32797
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.13 Å3/Da / Density % sol: 42.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 21% PEG 3350, 0.2M NaCl, 0.1M HEPES, 10mM DTT, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97856
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Dec 21, 2008
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.5→100 Å / Num. all: 8255 / Num. obs: 7955 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
SHARPphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.504→34.781 Å / SU ML: 0.3 / σ(F): 0.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2568 793 10.58 %RANDOM
Rwork0.2026 ---
obs0.2086 7492 90.88 %-
all-8282 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.297 Å2 / ksol: 0.365 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--17.7081 Å20 Å20 Å2
2--10.5151 Å2-0 Å2
3---7.1931 Å2
Refinement stepCycle: LAST / Resolution: 2.504→34.781 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1607 0 0 25 1632
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081632
X-RAY DIFFRACTIONf_angle_d1.1982193
X-RAY DIFFRACTIONf_dihedral_angle_d20.256611
X-RAY DIFFRACTIONf_chiral_restr0.089257
X-RAY DIFFRACTIONf_plane_restr0.004274
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.504-2.66110.3354830.277790X-RAY DIFFRACTION65
2.6611-2.86650.31631280.24581043X-RAY DIFFRACTION87
2.8665-3.15480.33191300.2141153X-RAY DIFFRACTION96
3.1548-3.61080.23431350.19891200X-RAY DIFFRACTION98
3.6108-4.54770.23891590.16371222X-RAY DIFFRACTION99
4.5477-34.78480.24561580.20811291X-RAY DIFFRACTION99

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