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BMRB: 18695

2LXT

Allosteric communication in the KIX domain proceeds through dynamic re-packing of the hydrophobic core

Authors

Bruschweiler, S., Schanda, P., Konrat, R., Tollinger, M.

Assembly

KIX domain complex (3)

Entity

1. KIX 1 (polymer, Thiol state: not present), 87 monomers, 10331.68 Da Detail

GVRKGWHEHV TQDLRSHLVH KLVQAIFPTP DPAALKDRRM ENLVAYAKKV EGDMYESANS RDEYYHLLAE KIYKIQKELE EKRRSRL

2. KIX 2 (polymer, Thiol state: not present), 19 monomers, 2060.327 Da Detail

DAGNILPSDI MDFVLKNTP

3. KIX 3 (polymer, Thiol state: not present), 34 monomers, 3937.230 Da Detail

DSVTDSQKRR EILSRRPXYR KILNDLSSDA PGVP

Total weight

16329.236 Da

Max. entity weight

10331.68 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 69.3 %, Completeness: 55.3 %, Completeness (bb): 64.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	55.3 % (921 of 1665)	55.5 % (488 of 880)	52.0 % (335 of 644)	69.5 % (98 of 141)
Backbone	64.2 % (525 of 818)	65.5 % (180 of 275)	61.2 % (252 of 412)	71.0 % (93 of 131)
Sidechain	48.4 % (475 of 981)	50.9 % (308 of 605)	44.3 % (162 of 366)	50.0 % (5 of 10)
Aromatic	48.0 % (48 of 100)	48.0 % (24 of 50)	49.0 % (24 of 49)	0.0 % (0 of 1)
Methyl	56.8 % (83 of 146)	56.2 % (41 of 73)	57.5 % (42 of 73)

1. KIX 1

GVRKGWHEHV TQDLRSHLVH KLVQAIFPTP DPAALKDRRM ENLVAYAKKV EGDMYESANS RDEYYHLLAE KIYKIQKELE EKRRSRL

2. KIX 2

DAGNILPSDI MDFVLKNTP

3. KIX 3

DSVTDSQKRR EILSRRPXYR KILNDLSSDA PGVP

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 5.8

#	Name	Isotope labeling	Type	Concentration
1	KIX_1	[U-100% 13C; U-100% 15N]		1 mM
2	KIX_2	natural abundance		2 mM
3	KIX_3	[U-100% 13C; U-100% 15N]		2 mM
4	sodium chloride	natural abundance		25 mM
5	potassium phosphate	natural abundance		50 mM
6	sodium azide	natural abundance		1 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2LXT, Strand ID: A, B, C Detail

Release date

2013-06-03

Citation

Allosteric communication in the KIX domain proceeds through dynamic repacking of the hydrophobic core
Bruschweiler, S., Konrat, R., Tollinger, M.
ACS Chem. Biol. (2013), 8, 1600-1610, PubMed 23651431 , DOI 10.1021/cb4002188 , Abstract

Related entities 1. KIX 1, : 6 : 23 entities Detail

Related entities 2. KIX 2, : 1 : 1 : 3 : 2 entities Detail

Related entities 3. KIX 3, : 9 : 9 entities Detail

Interaction partners 1. KIX 1, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Interaction partners 2. KIX 2, : 3 interactors Detail

More details for 3 interactors identified by 3 citations

Interaction partners 3. KIX 3, : 53 : 1 interactors Detail

More details for 54 interactors identified by 21 citations

Experiments performed 8 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 300 K, pH 5.8

#	Name	Isotope labeling	Type	Concentration
1	KIX_1	[U-100% 13C; U-100% 15N]		1 mM
2	KIX_2	natural abundance		2 mM
3	KIX_3	[U-100% 13C; U-100% 15N]		2 mM
4	sodium chloride	natural abundance		25 mM
5	potassium phosphate	natural abundance		50 mM
6	sodium azide	natural abundance		1 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

2 3D CBCA(CO)NH

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 5.8

#	Name	Isotope labeling	Type	Concentration
1	KIX_1	[U-100% 13C; U-100% 15N]		1 mM
2	KIX_2	natural abundance		2 mM
3	KIX_3	[U-100% 13C; U-100% 15N]		2 mM
4	sodium chloride	natural abundance		25 mM
5	potassium phosphate	natural abundance		50 mM
6	sodium azide	natural abundance		1 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

3 3D HN(CO)CA

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 5.8

#	Name	Isotope labeling	Type	Concentration
1	KIX_1	[U-100% 13C; U-100% 15N]		1 mM
2	KIX_2	natural abundance		2 mM
3	KIX_3	[U-100% 13C; U-100% 15N]		2 mM
4	sodium chloride	natural abundance		25 mM
5	potassium phosphate	natural abundance		50 mM
6	sodium azide	natural abundance		1 mM
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 300 K, pH 5.8

#	Name	Isotope labeling	Type	Concentration
1	KIX_1	[U-100% 13C; U-100% 15N]		1 mM
2	KIX_2	natural abundance		2 mM
3	KIX_3	[U-100% 13C; U-100% 15N]		2 mM
4	sodium chloride	natural abundance		25 mM
5	potassium phosphate	natural abundance		50 mM
6	sodium azide	natural abundance		1 mM
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 300 K, pH 5.8

#	Name	Isotope labeling	Type	Concentration
1	KIX_1	[U-100% 13C; U-100% 15N]		1 mM
2	KIX_2	natural abundance		2 mM
3	KIX_3	[U-100% 13C; U-100% 15N]		2 mM
4	sodium chloride	natural abundance		25 mM
5	potassium phosphate	natural abundance		50 mM
6	sodium azide	natural abundance		1 mM
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 300 K, pH 5.8

#	Name	Isotope labeling	Type	Concentration
1	KIX_1	[U-100% 13C; U-100% 15N]		1 mM
2	KIX_2	natural abundance		2 mM
3	KIX_3	[U-100% 13C; U-100% 15N]		2 mM
4	sodium chloride	natural abundance		25 mM
5	potassium phosphate	natural abundance		50 mM
6	sodium azide	natural abundance		1 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

7 3D 1H-15N NOESY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 5.8

#	Name	Isotope labeling	Type	Concentration
1	KIX_1	[U-100% 13C; U-100% 15N]		1 mM
2	KIX_2	natural abundance		2 mM
3	KIX_3	[U-100% 13C; U-100% 15N]		2 mM
4	sodium chloride	natural abundance		25 mM
5	potassium phosphate	natural abundance		50 mM
6	sodium azide	natural abundance		1 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

8 3D 1H-13C NOESY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 5.8

#	Name	Isotope labeling	Type	Concentration
1	KIX_1	[U-100% 13C; U-100% 15N]		1 mM
2	KIX_2	natural abundance		2 mM
3	KIX_3	[U-100% 13C; U-100% 15N]		2 mM
4	sodium chloride	natural abundance		25 mM
5	potassium phosphate	natural abundance		50 mM
6	sodium azide	natural abundance		1 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_18695_2lxt.nef
Input source #2: Coordindates	2lxt.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	True (see coodinates for details)
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)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
3:17:PRO:C	3:18:SEP:N	unknown	unknown	n/a
3:18:SEP:C	3:19:TYR:N	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
C	133	SEP	PHOSPHOSERINE	Assigned chemical shifts, Coordinates

Sequence alignments

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

--590-------600-------610-------620-------630-------640-------650-------660-------670--
GVRKGWHEHVTQDLRSHLVHKLVQAIFPTPDPAALKDRRMENLVAYAKKVEGDMYESANSRDEYYHLLAEKIYKIQKELEEKRRSRL
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GVRKGWHEHVTQDLRSHLVHKLVQAIFPTPDPAALKDRRMENLVAYAKKVEGDMYESANSRDEYYHLLAEKIYKIQKELEEKRRSRL
--------10--------20--------30--------40--------50--------60--------70--------80-------

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

840-----850--------
DAGNILPSDIMDFVLKNTP
|||||||||||||||||||
DAGNILPSDIMDFVLKNTP
--------10---------

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

--120-------130-------140---------
DSVTDSQKRREILSRRPXYRKILNDLSSDAPGVP
||||||||||||||||||||||||||||||||||
DSVTDSQKRREILSRRPXYRKILNDLSSDAPGVP
--------10--------20--------30----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	87	0	0	100.0
B	B	19	0	0	100.0
C	C	34	0	0	100.0

Content subtype: combined_18695_2lxt.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	2		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	883		69.0 (chain: A, length: 87), 94.1 (chain: C, length: 34)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	1028 (1)	noe	98.9 (chain: A, length: 87), 89.5 (chain: B, length: 19), 85.3 (chain: C, length: 34)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	216 (216)	.	96.6 (chain: A, length: 87), 57.9 (chain: B, length: 19), 88.2 (chain: C, length: 34)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_4	OK	100 (100)	.	89.7 (chain: A, length: 87), 61.8 (chain: C, length: 34)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 87, Sequence coverage: 69.0%
  - Entity_assembly_ID: C, Chain length: 34, Sequence coverage: 94.1%
- Total number of assignments
  - ¹H chemical shifts: 468
  - ¹³C chemical shifts: 323
  - ¹⁵N chemical shifts: 92
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: C
- 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
  - Chain_ID: C

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 87, Sequence coverage: 98.9%
  - Entity_assembly_ID: B, Chain length: 19, Sequence coverage: 89.5%
  - Entity_assembly_ID: C, Chain length: 34, Sequence coverage: 85.3%
- Total number of restraints: 1028
- Weight of restraints: 1.0 (1028)
- Potential type of restraints: square-well-parabolic (1028)
- Range of distance target values: 1.46, 5.1 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
  - Chain_ID: C
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 87, Sequence coverage: 96.6%
  - Entity_assembly_ID: B, Chain length: 19, Sequence coverage: 57.9%
  - Entity_assembly_ID: C, Chain length: 34, Sequence coverage: 88.2%
- Total number of restraints: 216
- Total number of restraints per polymer type: 216
- Weight of restraints: 1.0 (216)
- Potential type of restraints: square-well-parabolic (216)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B
  - Chain_ID: C

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 87, Sequence coverage: 89.7%
  - Entity_assembly_ID: C, Chain length: 34, Sequence coverage: 61.8%
- Total number of restraints: 100
- Potential type of restraints: undefined (100)
- Range of observed RDC values: 100.0, -100.0 (Hz)
- RDC restraints per residue
  - Chain_ID: A
    None
  - Chain_ID: C
    None

Keywords CREB binding protein, mixed-lineage leukemia activation domain, phosphorylated kinase inducible domain of CREB, ternary complex