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Found 1 Document (1.049 seconds)

BMRB: 18522

2LUI

Chemical Shift Assignments for the PICK1 PDZ domain fused to the C10 DAT ligand

Authors

Erlendsson, S., Teilum, K.

Assembly

PICK1 PDZ domain fused to the C10 DAT ligand

Entity

1. PICK1 PDZ domain fused to the C10 DAT ligand (polymer), 232 monomers, 24810.40 Da Detail

GSPGIPVPGK VTLQKDAQNL IGISIGGGAQ YCPCLYIVQV FDNTPAALDG TVAAGDEITG VNGRSIKGKT KVEVAKMIQE VKGEVTIHYN KLQADPKQLE VLFQGPQFTL RHWLKVGSPG IPVPGKVTLQ KDAQNLIGIS IGGGAQYCPC LYIVQVFDNT PAALDGTVAA GDEITGVNGR SIKGKTKVEV AKMIQEVKGE VTIHYNKLQA DPKQLEVLFQ GPQFTLRHWL KV

Formula weight

24810.4 Da

Source organism

Rattus norvegicus

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 59.9 %, Completeness: 46.1 %, Completeness (bb): 54.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	46.1 % (1230 of 2670)	44.5 % (617 of 1386)	46.5 % (483 of 1038)	52.8 % (130 of 246)
Backbone	54.2 % (739 of 1364)	53.6 % (256 of 478)	54.0 % (361 of 668)	56.0 % (122 of 218)
Sidechain	39.8 % (601 of 1510)	39.8 % (361 of 908)	40.4 % (232 of 574)	28.6 % (8 of 28)
Aromatic	13.5 % (20 of 148)	18.9 % (14 of 74)	6.9 % (5 of 72)	50.0 % (1 of 2)
Methyl	49.3 % (148 of 300)	51.3 % (77 of 150)	47.3 % (71 of 150)

1. entity

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	TRIS	natural abundance	50 mM
2	sodium chloride	natural abundance	125 mM
3	DTT	natural abundance	2 mM
4	protein	[U-100% 13C; U-100% 15N]	600 uM
5	DSS	natural abundance	0.25 mM
6	sodium azide	natural abundance	0.01 %
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 7.4

#	Name	Isotope labeling	Concentration
9	TRIS	[U-99% 2H]	50 mM
10	sodium chloride	natural abundance	125 mM
11	DTT	natural abundance	2 mM
12	protein	[U-100% 13C; U-100% 15N]	600 uM
13	DSS	natural abundance	0.25 mM
14	sodium azide	natural abundance	0.01 %
15	D2O	natural abundance	100 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.23 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.23 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.02 ppm, Outliers: 2 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.04 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2LUI, Strand ID: A Detail

Release date

2012-06-20

Citation

Protein interacting with C-kinase 1 (PICK1) binding promiscuity relies on unconventional PSD-95/discs-large/ZO-1 homology (PDZ) binding modes for nonclass II PDZ ligands
Erlendsson, S., Rathje, M., Heidarsson, P.O., Poulsen, F.M., Madsen, K.L., Teilum, K., Gether, U.
J. Biol. Chem. (2014), 289, 25327-25340, PubMed 25023278 , DOI 10.1074/jbc.M114.548743 , Abstract

Related entities 1. PICK1 PDZ domain fused to the C10 DAT ligand, : 122 entities Detail

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	TRIS	natural abundance	50 mM
2	sodium chloride	natural abundance	125 mM
3	DTT	natural abundance	2 mM
4	protein	[U-100% 13C; U-100% 15N]	600 uM
5	DSS	natural abundance	0.25 mM
6	sodium azide	natural abundance	0.01 %
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

2 2D 1H-13C HSQC

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 7.4

#	Name	Isotope labeling	Concentration
9	TRIS	[U-99% 2H]	50 mM
10	sodium chloride	natural abundance	125 mM
11	DTT	natural abundance	2 mM
12	protein	[U-100% 13C; U-100% 15N]	600 uM
13	DSS	natural abundance	0.25 mM
14	sodium azide	natural abundance	0.01 %
15	D2O	natural abundance	100 %

3 3D CBCA(CO)NH

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	TRIS	natural abundance	50 mM
2	sodium chloride	natural abundance	125 mM
3	DTT	natural abundance	2 mM
4	protein	[U-100% 13C; U-100% 15N]	600 uM
5	DSS	natural abundance	0.25 mM
6	sodium azide	natural abundance	0.01 %
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

4 3D HNCO

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	TRIS	natural abundance	50 mM
2	sodium chloride	natural abundance	125 mM
3	DTT	natural abundance	2 mM
4	protein	[U-100% 13C; U-100% 15N]	600 uM
5	DSS	natural abundance	0.25 mM
6	sodium azide	natural abundance	0.01 %
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

5 3D HNCA

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	TRIS	natural abundance	50 mM
2	sodium chloride	natural abundance	125 mM
3	DTT	natural abundance	2 mM
4	protein	[U-100% 13C; U-100% 15N]	600 uM
5	DSS	natural abundance	0.25 mM
6	sodium azide	natural abundance	0.01 %
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

6 3D HNCACB

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	TRIS	natural abundance	50 mM
2	sodium chloride	natural abundance	125 mM
3	DTT	natural abundance	2 mM
4	protein	[U-100% 13C; U-100% 15N]	600 uM
5	DSS	natural abundance	0.25 mM
6	sodium azide	natural abundance	0.01 %
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

7 3D HN(CO)CA

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	TRIS	natural abundance	50 mM
2	sodium chloride	natural abundance	125 mM
3	DTT	natural abundance	2 mM
4	protein	[U-100% 13C; U-100% 15N]	600 uM
5	DSS	natural abundance	0.25 mM
6	sodium azide	natural abundance	0.01 %
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

8 3D HCCH-TOCSY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	TRIS	natural abundance	50 mM
2	sodium chloride	natural abundance	125 mM
3	DTT	natural abundance	2 mM
4	protein	[U-100% 13C; U-100% 15N]	600 uM
5	DSS	natural abundance	0.25 mM
6	sodium azide	natural abundance	0.01 %
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

9 3D 1H-15N NOESY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	TRIS	natural abundance	50 mM
2	sodium chloride	natural abundance	125 mM
3	DTT	natural abundance	2 mM
4	protein	[U-100% 13C; U-100% 15N]	600 uM
5	DSS	natural abundance	0.25 mM
6	sodium azide	natural abundance	0.01 %
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

10 3D 1H-13C NOESY aliphatic

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 7.4

#	Name	Isotope labeling	Concentration
9	TRIS	[U-99% 2H]	50 mM
10	sodium chloride	natural abundance	125 mM
11	DTT	natural abundance	2 mM
12	protein	[U-100% 13C; U-100% 15N]	600 uM
13	DSS	natural abundance	0.25 mM
14	sodium azide	natural abundance	0.01 %
15	D2O	natural abundance	100 %

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18522_2lui.nef
Input source #2: Coordindates	2lui.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

------20--------30--------40--------50--------60--------70--------80--------90-------100-------110--
GSPGIPVPGKVTLQKDAQNLIGISIGGGAQYCPCLYIVQVFDNTPAALDGTVAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVTIHYNKLQADPKQLE
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSPGIPVPGKVTLQKDAQNLIGISIGGGAQYCPCLYIVQVFDNTPAALDGTVAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVTIHYNKLQADPKQLE
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

-----120--------
VLFQGPQFTLRHWLKV
||||||||||||||||
VLFQGPQFTLRHWLKV
-------110------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	116	0	0	100.0

Content subtype: combined_18522_2lui.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	chemical_shift_list	Warning	996		95.7 (chain: A, length: 116)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	223 (1)	noe	44.8 (chain: A, length: 116)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	1076 (1)	noe	90.5 (chain: A, length: 116)
3	Distance restraints	CNS/XPLOR_distance_constraints_5	OK	39 (1)	hbond	45.7 (chain: A, length: 116)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	66 (66)	.	50.0 (chain: A, length: 116)

Assigned chemical shifts

Saveframe: chemical_shift_list
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 116, Sequence coverage: 95.7%
- Total number of assignments
  - ¹³C chemical shifts: 382
  - ¹H chemical shifts: 508
  - ¹⁵N chemical shifts: 106
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
36	SER	HG	5.907
56	THR	HG1	5.031
83	LYS	HZ1	7.633
83	LYS	HZ2	7.633
83	LYS	HZ3	7.633
98	THR	HG1	5.193
127	LYS	HZ1	7.439
127	LYS	HZ2	7.439
127	LYS	HZ3	7.439

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	519	382	73.6
¹H chemical shifts	693	499	72.0
¹⁵N chemical shifts	125	106	84.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	232	208	89.7
¹H chemical shifts	239	208	87.0
¹⁵N chemical shifts	109	98	89.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	287	174	60.6
¹H chemical shifts	454	291	64.1
¹⁵N chemical shifts	16	8	50.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	76	53	69.7
¹H chemical shifts	76	65	85.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	36	0	0.0
¹H chemical shifts	37	9	24.3
¹⁵N chemical shifts	1	1	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 116, Sequence coverage: 44.8%
- Total number of restraints: 223
- Weight of restraints: 1.0 (223)
- Potential type of restraints: square-well-parabolic (223)
- Range of distance target values: 2.16, 3.5 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: Warning
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 116, Sequence coverage: 90.5%
  - Total number of restraints: 1076
  - Weight of restraints: 1.0 (1076)
  - Potential type of restraints: square-well-parabolic (1076)
  - Range of distance target values: 1.83, 4.5 (Å)
  - Histogram of distance target values
  - Histogram of discrepancy in distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map
  - Saveframe: CNS/XPLOR_distance_constraints_5
    - Status: OK
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 116, Sequence coverage: 45.7%
    - Total number of restraints: 39
    - Weight of restraints: 1.0 (39)
    - Potential type of restraints: square-well-parabolic (39)
    - Range of distance target values: 1.97, 2.21 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
    - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 116, Sequence coverage: 50.0%
- Total number of restraints: 66
- Total number of restraints per polymer type: 66
- Weight of restraints: 1.0 (66)
- Potential type of restraints: square-well-parabolic (66)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords DAT C-terminal, PDZ, PICK1

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Found 1 Document (1.049 seconds)

BMRB: 18522

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. PICK1 PDZ domain fused to the C10 DAT ligand, : 122 entities Detail

Experiments performed 10 experiments Detail

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NMR combined restraints 6 contents Detail