Mass: 18994.729 Da / Num. of mol.: 1 Fragment: FAT DOMAIN, UNP RESIDUES 916-1053, LINKER, LD2, UNP RESIDUES 140-161 Source method: isolated from a genetically manipulated source Details: Fat domain of focal adhesion kinase with the ld2 motif of paxillin tethered via linker GSGGSGSGGSGGSG Source: (gene. exp.) Gallus gallus, unidentified / Gene: PTK2, FAK, FAK1, PXN / Plasmid: pET28A / Organelle (production host): 469008 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: Q00944, UniProt: P49024, non-specific protein-tyrosine kinase
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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 1H-15N NOESY
1
2
1
3D 1H-13C NOESY
1
3
1
3D (H)CCH-TOCSY
1
4
1
3D (H)CCH-COSY
1
5
1
3D HNCA
1
6
1
3DCBCA(CO)NH
1
7
1
3D HNCO
1
8
1
3D HN(CA)CB
1
9
1
2D 1H-15N HSQC
1
10
1
2D 1H-13C HSQC
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Sample preparation
Details
Contents: 1 mM [U-100% 13C; U-100% 15N] FOCAL ADHESION KINASE 1, LINKER, 22-MERIC PEPTIDE FROM PAXILLIN-1, 10 mM potassium phosphate-2, 0.1 % sodium azide-3, 5 mM LD4 PEPTIDE FROM PAXILLIN-4, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)
Component
Isotopic labeling
Solution-ID
1mM
FOCAL ADHESION KINASE 1, LINKER, 22-MERIC PEPTIDE FROM PAXILLIN-1
[U-100% 13C; U-100% 15N]
1
10mM
potassium phosphate-2
1
0.1 %
sodium azide-3
1
5mM
LD4 PEPTIDE FROM PAXILLIN-4
1
Sample conditions
Ionic strength: 10 / pH: 6.5 / Pressure: AMBIENT Pa / Temperature: 310 K
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NMR measurement
NMR spectrometer
Type
Manufacturer
Model
Field strength (MHz)
Spectrometer-ID
BRUKER AVANCE
Bruker
AVANCE
800
1
VARIAN INOVA
Varian
INOVA
600
2
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Processing
NMR software
Name
Developer
Classification
CYANA
Guntert, MumenthalerandWuthrich
refinement
CYANA
Guntert, MumenthalerandWuthrich
structuresolution
Sparky
Goddard
structuresolution
NMRPipe
Delaglio, Grzesiek, Vuister, Zhu, PfeiferandBax
structuresolution
MOLMOL
Koradi, BilleterandWuthrich
structuresolution
Refinement
Method: SIMULATED ANNEALING, TORSION ANGLE DYNAMICS / Software ordinal: 1 Details: THE SAMPLES USED ARE CONSTRUCTS IN WHICH ONE MOTIF IS TETHERED TO THE C-TERMINUS OF THE FAT DOMAIN VIA A GGSX LINKER AND THE OTHER LD MOTIF IS BOUND AS A FREE PEPTIDE. THE GGS LINKERS ARE ...Details: THE SAMPLES USED ARE CONSTRUCTS IN WHICH ONE MOTIF IS TETHERED TO THE C-TERMINUS OF THE FAT DOMAIN VIA A GGSX LINKER AND THE OTHER LD MOTIF IS BOUND AS A FREE PEPTIDE. THE GGS LINKERS ARE UNSTRUCTURED AND COMPARISON OF SPECTRA LEAD US TO BELIEVE THEY DO NOT IMPOSE ANY CONSTRAINT UPON HOW THE TETHERED LD MOTIFS BIND TO FAT. HOWEVER WHEN ANALYZING THE STRUCTURE IN CYANA, THE PRESENCE OF THE GGS LINKER IN THE SEQUENCE INTERFERS WITH CYANA'S INITIAL ALIGNMENT OF THE 20 LOWEST ENERGY STRUCTURES AND THUS CONFUSES RMSD AND TARGET FUNCTION CALCULATIONS. WE FOUND THAT USING PSEUDO LINKERS IN CYANA RESOLVED THIS PROBLEM WITHOUT CHANGING THE STRUCTURES IN QUESTION AND SO WE CHOSE TO SUBMIT THE STRUCTURES IN THAT WAY. 2RP6 REPRESENTS A COMPOSITE STRUCTURE USING CONSTRAINTS OBTAINED FROM THE 2RP7 AND 2RP9 DATA SETS. IT DOES NOT REPRESENT A NEW CONSTRUCT IN ITSELF, BUT MOST ACCURATELY REPRESENTS THE COMPLETE COMPLEX STRUCTURE BETWEEN PAXILLIN AND FOCAL ADHESION KINASE.
NMR representative
Selection criteria: lowest energy
NMR ensemble
Conformer selection criteria: target function / Conformers calculated total number: 500 / Conformers submitted total number: 20
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