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BMRB: 15928

2K7S

Human ARNT C-Terminal PAS Domain, 3 Residue IB slip

Authors

Evans, M.R., Card, P.B., Gardner, K.H.

Assembly

ARNT PAS-B Slipped IB Strand

Entity

1. ARNT PAS-B Slipped IB Strand (polymer, Thiol state: all free), 119 monomers, 13785.37 Da Detail

GAMDNVCQPT EFISRHNIEG IFTFVDHRCV ATVGYQPQEL LGKNIVEFCH PEDQQLLRDS FQQVVKLKGQ VLSVMFRFRS KNQEWLWMRT SSQTAQNPYS DEIETIICTN TNVKNSSQE

Formula weight

13785.37 Da

Source organism

Exptl. method

Refine. method

simulated annealing, torsion angle dynamics, molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 95.8 %, Completeness: 89.7 %, Completeness (bb): 90.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	89.7 % (1277 of 1424)	88.7 % (660 of 744)	91.5 % (497 of 543)	87.6 % (120 of 137)
Backbone	90.8 % (641 of 706)	90.8 % (217 of 239)	90.1 % (317 of 352)	93.0 % (107 of 115)
Sidechain	89.4 % (744 of 832)	87.7 % (443 of 505)	94.4 % (288 of 305)	59.1 % (13 of 22)
Aromatic	97.5 % (119 of 122)	98.4 % (60 of 61)	96.6 % (57 of 59)	100.0 % (2 of 2)
Methyl	96.6 % (114 of 118)	96.6 % (57 of 59)	96.6 % (57 of 59)

1. ARNT PAS-B Slipped IB Strand

GAMDNVCQPT EFISRHNIEG IFTFVDHRCV ATVGYQPQEL LGKNIVEFCH PEDQQLLRDS FQQVVKLKGQ VLSVMFRFRS KNQEWLWMRT SSQTAQNPYS DEIETIICTN TNVKNSSQE

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 5mM DTT

#	Name	Isotope labeling	Type	Concentration
1	ARNT PAS-B Slipped IB Strand	[U-98% 13C; U-98% 15N]		900 uM
2	TRIS	natural abundance		50 mM
3	sodium chloride	natural abundance		17 mM
4	DTT	natural abundance		5 mM
5	H2O	natural abundance		90 %
6	D2O	[U-100% 2H]		10 %

LACS Plot; CA

Referencing offset: -0.03 ppm, Outliers: 3 Detail

LACS Plot; CB

Referencing offset: -0.03 ppm, Outliers: 3 Detail

LACS Plot; HA

Referencing offset: -0.03 ppm, Outliers: 2 Detail

LACS Plot; CO

Referencing offset: 0.24 ppm, Outliers: 5 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2K7S, Strand ID: A Detail

Release date

2008-02-12

Citation 1

ARNT PAS-B has a fragile native state structure with an alternative beta-sheet register nearby in sequence space
Evans, M.R., Card, P.B., Gardner, K.H.
Proc. Natl. Acad. Sci. U. S. A. (2009), 106, 2617-2622, PubMed 19196990 , DOI 10.1073/pnas.0808270106 , Abstract

Show more 1 citaion

Citation 2

Structural basis of ARNT PAS-B dimerization: use of a common beta-sheet interface for hetero- and homodimerization
Card, P.B., Erbel, P.J. A., Gardner, K.H.
J. Mol. Biol. (2005), 353, 664-677, PubMed 16181639 , DOI 10.1016/j.jmb.2005.08.043 , Abstract

Hide non-primary 1 citaion

Related entities 1. ARNT PAS-B Slipped IB Strand, : 1 : 29 : 238 entities Detail

Interaction partners 1. ARNT PAS-B Slipped IB Strand, : 29 interactors Detail

More details for 29 interactors identified by 10 citations

Experiments performed 9 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 5mM DTT

#	Name	Isotope labeling	Type	Concentration
1	ARNT PAS-B Slipped IB Strand	[U-98% 13C; U-98% 15N]		900 uM
2	TRIS	natural abundance		50 mM
3	sodium chloride	natural abundance		17 mM
4	DTT	natural abundance		5 mM
5	H2O	natural abundance		90 %
6	D2O	[U-100% 2H]		10 %

2 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 5mM DTT

#	Name	Isotope labeling	Type	Concentration
1	ARNT PAS-B Slipped IB Strand	[U-98% 13C; U-98% 15N]		900 uM
2	TRIS	natural abundance		50 mM
3	sodium chloride	natural abundance		17 mM
4	DTT	natural abundance		5 mM
5	H2O	natural abundance		90 %
6	D2O	[U-100% 2H]		10 %

3 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 5mM DTT

#	Name	Isotope labeling	Type	Concentration
1	ARNT PAS-B Slipped IB Strand	[U-98% 13C; U-98% 15N]		900 uM
2	TRIS	natural abundance		50 mM
3	sodium chloride	natural abundance		17 mM
4	DTT	natural abundance		5 mM
5	H2O	natural abundance		90 %
6	D2O	[U-100% 2H]		10 %

4 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 5mM DTT

#	Name	Isotope labeling	Type	Concentration
1	ARNT PAS-B Slipped IB Strand	[U-98% 13C; U-98% 15N]		900 uM
2	TRIS	natural abundance		50 mM
3	sodium chloride	natural abundance		17 mM
4	DTT	natural abundance		5 mM
5	H2O	natural abundance		90 %
6	D2O	[U-100% 2H]		10 %

5 3D HNCO

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 5mM DTT

#	Name	Isotope labeling	Type	Concentration
1	ARNT PAS-B Slipped IB Strand	[U-98% 13C; U-98% 15N]		900 uM
2	TRIS	natural abundance		50 mM
3	sodium chloride	natural abundance		17 mM
4	DTT	natural abundance		5 mM
5	H2O	natural abundance		90 %
6	D2O	[U-100% 2H]		10 %

6 2D 1H-1H TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 5mM DTT

#	Name	Isotope labeling	Type	Concentration
1	ARNT PAS-B Slipped IB Strand	[U-98% 13C; U-98% 15N]		900 uM
2	TRIS	natural abundance		50 mM
3	sodium chloride	natural abundance		17 mM
4	DTT	natural abundance		5 mM
5	H2O	natural abundance		90 %
6	D2O	[U-100% 2H]		10 %

7 2D 1H-1H NOESY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 5mM DTT

#	Name	Isotope labeling	Type	Concentration
1	ARNT PAS-B Slipped IB Strand	[U-98% 13C; U-98% 15N]		900 uM
2	TRIS	natural abundance		50 mM
3	sodium chloride	natural abundance		17 mM
4	DTT	natural abundance		5 mM
5	H2O	natural abundance		90 %
6	D2O	[U-100% 2H]		10 %

8 3D 1H-13C NOESY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 5mM DTT

#	Name	Isotope labeling	Type	Concentration
1	ARNT PAS-B Slipped IB Strand	[U-98% 13C; U-98% 15N]		900 uM
2	TRIS	natural abundance		50 mM
3	sodium chloride	natural abundance		17 mM
4	DTT	natural abundance		5 mM
5	H2O	natural abundance		90 %
6	D2O	[U-100% 2H]		10 %

9 3D 1H-15N NOESY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 5mM DTT

#	Name	Isotope labeling	Type	Concentration
1	ARNT PAS-B Slipped IB Strand	[U-98% 13C; U-98% 15N]		900 uM
2	TRIS	natural abundance		50 mM
3	sodium chloride	natural abundance		17 mM
4	DTT	natural abundance		5 mM
5	H2O	natural abundance		90 %
6	D2O	[U-100% 2H]		10 %

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15928_2k7s.nef
Input source #2: Coordindates	2k7s.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

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

-------110---------
DEIETIICTNTNVKNSSQE
|||||||||||||||||||
DEIETIICTNTNVKNSSQE

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	119	0	0	100.0

Content subtype: combined_15928_2k7s.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1280		95.0 (chain: A, length: 119)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	1253 (1)	noe	89.9 (chain: A, length: 119)
2	Distance restraints	CNS/XPLOR_distance_constraints_5	Warning	3082 (1)	noe	91.6 (chain: A, length: 119)
3	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	100 (1)	hbond	53.8 (chain: A, length: 119)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	133 (133)	.	72.3 (chain: A, length: 119)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 119, Sequence coverage: 95.0%
- Total number of assignments
  - ¹H chemical shifts: 666
  - ¹³C chemical shifts: 492
  - ¹⁵N chemical shifts: 122
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Tautomeric state of HIS
- 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

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 119, Sequence coverage: 89.9%
- Total number of restraints: 1252
- Weight of restraints: 1.0 (1252)
- Potential type of restraints: square-well-parabolic (1252)
- Range of distance target values: 1.62, 3.77 (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: Warning
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 119, Sequence coverage: 91.6%
  - Total number of restraints: 3082
  - Weight of restraints: 1.0 (3082)
  - Potential type of restraints: square-well-parabolic (3082)
  - Range of distance target values: 1.66, 4.25 (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_4
    - Status: OK
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 119, Sequence coverage: 53.8%
    - Total number of restraints: 100
    - Weight of restraints: 1.0 (100)
    - Potential type of restraints: square-well-parabolic (100)
    - Range of distance target values: 2.05, 3.05 (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_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 119, Sequence coverage: 72.3%
- Total number of restraints: 133
- Total number of restraints per polymer type: 133
- Weight of restraints: 1.0 (133)
- Potential type of restraints: square-well-parabolic (133)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords ARNT PAS-B, Beta-strand Slip, PAS domain