- PDB-1kxl: Solution Structure of the Cdc13 DNA-binding Domain in a Complex w... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 1kxl
Title
Solution Structure of the Cdc13 DNA-binding Domain in a Complex with Single-Stranded Telomeric DNA (DNA structure not modeled)
Components
CELL DIVISION CONTROL PROTEIN 13
Keywords
CELL CYCLE / DNA-binding domain / telomere / single-stranded DNA / OB fold
Function / homology
Function and homology information
CST complex / ribonucleoprotein complex localization / telomerase inhibitor activity / translation elongation factor binding / regulation of telomere maintenance via telomerase / nuclear telomere cap complex / single-stranded telomeric DNA binding / 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 / nuclear telomere cap complex / single-stranded telomeric DNA binding / G-rich strand telomeric DNA binding / telomere capping / telomere maintenance via telomerase / telomere maintenance / chromosome, telomeric region / cell cycle / cell division / identical protein binding Similarity search - Function
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 ...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 / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta Similarity search - Domain/homology
structures with the least restraint violations, structures with the lowest energy
Representative
Model #10
closest to the average
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Components
#1: Protein
CELLDIVISIONCONTROLPROTEIN13
Mass: 23575.127 Da / Num. of mol.: 1 / Fragment: DNA-binding domain (residues 497-694) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Plasmid: pET21a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P32797
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Experimental details
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Experiment
Experiment
Method: SOLUTION NMR
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Type
1
1
1
3D 15N-separated NOESY
1
2
2
3D 13C-separated NOESY
1
3
1
4D 13C/15N-separated NOESY
2
4
2
4D 13C-separated NOESY
NMR details
Text: Representative conformer was structure closest to the mean.
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Sample preparation
Details
Solution-ID
Solvent system
1
90% H2O/10% D2O
2
100% D2O
Sample conditions
Conditions-ID
pH
Pressure (kPa)
Temperature (K)
1
7.0
ambient
303K
2
7.0
ambient
308K
Crystal grow
*PLUS
Method: other / Details: NMR
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NMR measurement
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelength
Relative weight: 1
NMR spectrometer
Type
Manufacturer
Model
Field strength (MHz)
Spectrometer-ID
Varian INOVA
Varian
INOVA
600
1
Varian INOVA
Varian
INOVA
500
2
Bruker DRX
Bruker
DRX
800
3
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Processing
NMR software
Name
Version
Developer
Classification
NMRPipe
Delaglio
processing
ANSIG
3.3
Kraulis
dataanalysis
X-PLOR
3.851
Brunger
structuresolution
X-PLOR
3.851
Brunger
refinement
Refinement
Method: distance geometry, simulated annealing, molecular dynamics Software ordinal: 1 Details: DNA STRUCTURE NOT MODELED DUE TO CHEMICAL SHIFT ASSIGNMENT AMBIGUITY.
NMR representative
Selection criteria: closest to the average
NMR ensemble
Conformer selection criteria: structures with the least restraint violations, structures with the lowest energy Conformers calculated total number: 50 / Conformers submitted total number: 10
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