- PDB-2kqd: First PBZ domain of human APLF protein in complex with ribofurano... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 2kqd
Title
First PBZ domain of human APLF protein in complex with ribofuranosyladenosine
Components
Aprataxin and PNK-like factor
Keywords
LYASE / ADP-ribosylation / DNA damage / DNA repair / Metal-binding / Nucleotide-binding / Nucleus / Zinc / Zinc-finger
Function / homology
Function and homology information
ADP-D-ribose modification-dependent protein binding / regulation of isotype switching / histone chaperone activity / poly-ADP-D-ribose binding / positive regulation of DNA ligation / regulation of epithelial to mesenchymal transition / single strand break repair / DNA repair-dependent chromatin remodeling / site of DNA damage / protein folding chaperone ...ADP-D-ribose modification-dependent protein binding / regulation of isotype switching / histone chaperone activity / poly-ADP-D-ribose binding / positive regulation of DNA ligation / regulation of epithelial to mesenchymal transition / single strand break repair / DNA repair-dependent chromatin remodeling / site of DNA damage / protein folding chaperone / DNA-(apurinic or apyrimidinic site) endonuclease activity / protein localization to chromatin / embryo implantation / 3'-5' exonuclease activity / DNA endonuclease activity / double-strand break repair via nonhomologous end joining / double-strand break repair / site of double-strand break / histone binding / Hydrolases; Acting on ester bonds / DNA repair / nucleotide binding / DNA damage response / nucleoplasm / nucleus / metal ion binding / cytosol Similarity search - Function
Type: D-saccharide, alpha linking / Mass: 150.130 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Formula: C5H10O5
Identifier
Type
Program
DRibfa
CONDENSED IUPAC CARBOHYDRATE SYMBOL
GMML 1.0
a-D-ribofuranose
COMMON NAME
GMML 1.0
a-D-Ribf
IUPAC CARBOHYDRATE SYMBOL
PDB-CARE 1.0
Rib
SNFG CARBOHYDRATE SYMBOL
GMML 1.0
Compound details
RESIDUES 418-451 ARE NOT SHOWN IN THE COORDINATES BECAUSE STRUCTURE CALCULATIONS WERE CARRIED OUT ...RESIDUES 418-451 ARE NOT SHOWN IN THE COORDINATES BECAUSE STRUCTURE CALCULATIONS WERE CARRIED OUT ON RESIDUES 363-417 ONLY.
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Experimental details
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Experiment
Experiment
Method: SOLUTION NMR
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Type
3
1
1
2D 1H-15N HSQC
1
2
2
2D 1H-13C HSQC full-width
1
3
2
2D 1H-1H NOESY
1
4
2
2D 1H-1H NOESY filtered
1
5
2
3D 1H-13C NOESY
1
6
2
2D 1H-1H TOCSY
2
7
2
2D 1H-13C HSQC full-width
2
8
2
2D 1H-1H NOESY
2
9
2
2D 1H-1H NOESY filtered
2
10
2
3D 1H-13C NOESY
2
11
2
2D 1H-1H TOCSY
NMR details
Text: The author states that NMR was carried out on a single fragment (363-451) containing both fingers F1 and F2 of APLF, but the structure calculations were carried out separately for each finger. ...Text: The author states that NMR was carried out on a single fragment (363-451) containing both fingers F1 and F2 of APLF, but the structure calculations were carried out separately for each finger. This co-ordinate file includes residues 363-417 and contains F1 as well as the unstructured regions on either side.
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Sample preparation
Details
Solution-ID
Contents
Solvent system
1
20 mM potassium pyrophosphate, 200 mM sodium chloride, 100 uM zinc sulphate, 2 mM [U-2H] DTT, 0.8 mM [U-98% 13C; U-98% 15N] APLF_363-451, 2 mM RFA, 95% H2O/5% D2O
95% H2O/5% D2O
2
20 mM potassium pyrophosphate, 200 mM sodium chloride, 100 uM zinc sulphate, 2 mM [U-2H] DTT, 0.8 mM [U-98% 13C; U-98% 15N] APLF_363-451, 2 mM RFA, 100% D2O
100% D2O
Sample
Conc. (mg/ml)
Component
Isotopic labeling
Solution-ID
20mM
potassium pyrophosphate-1
1
200mM
sodium chloride-2
1
100uM
zinc sulphate-3
1
2mM
DTT-4
[U-2H]
1
0.8mM
APLF_363-451-5
[U-98% 13C; U-98% 15N]
1
2mM
RFA-6
1
20mM
potassium pyrophosphate-7
2
200mM
sodium chloride-8
2
100uM
zinc sulphate-9
2
2mM
DTT-10
[U-2H]
2
0.8mM
APLF_363-451-11
[U-98% 13C; U-98% 15N]
2
2mM
RFA-12
2
Sample conditions
Conditions-ID
Ionic strength
pH
Pressure (kPa)
Temperature (K)
1
0.4
6.0
ambient
278K
2
0.4
6.0
ambient
286K
3
0.4
6.0
ambient
300K
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NMR measurement
NMR spectrometer
Type
Manufacturer
Model
Field strength (MHz)
Spectrometer-ID
Bruker Avance
Bruker
AVANCE
800
1
Bruker DMX
Bruker
DMX
600
2
Bruker DRX
Bruker
DRX
500
3
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Processing
NMR software
Name
Developer
Classification
XPLOR-NIH
Schwieters, Kuszewski, TjandraandClore
structuresolution
XPLOR-NIH
Schwieters, Kuszewski, TjandraandClore
refinement
Refinement
Method: simulated annealing / Software ordinal: 1
NMR constraints
Protein chi angle constraints total count: 11 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 12 / Protein psi angle constraints total count: 13
NMR representative
Selection criteria: lowest energy
NMR ensemble
Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 50 / Conformers submitted total number: 10 / Maximum torsion angle constraint violation: 5.7 ° / Maximum upper distance constraint violation: 0.59 Å / Torsion angle constraint violation method: XPLOR-NIH
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