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BMRB: 16348

2KK0

SOLUTION STRUCTURE OF DEAD RINGER-LIKE PROTEIN 1 (AT-RICH INTERACTIVE DOMAIN-CONTAINING PROTEIN 3A) FROM HOMO SAPIENS, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) TARGET HR4394C

Authors

Liu, G., Wang, D., NWOSU, C., OWENS, L., Xiao, R., Liu, J., Baran, M.C., Swapna, G., Acton, T.B., Rost, B., Montelione, G.T.

Assembly

DEAD RINGER-LIKE PROTEIN 1

Entity

1. DEAD RINGER-LIKE PROTEIN 1 (polymer, Thiol state: all free), 145 monomers, 17133.42 Da Detail

MGHHHHHHSH MPDHGDWTYE EQFKQLYELD GDPKRKEFLD DLFSFMQKRG TPVNRIPIMA KQVLDLFMLY VLVTEKGGLV EVINKKLWRE ITKGLNLPTS ITSAAFTLRT QYMKYLYPYE CEKRGLSNPN ELQAAIDSNR REGRR

Formula weight

17133.42 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

molecular dynamics, distance geometry, simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 93.8 %, Completeness: 88.2 %, Completeness (bb): 88.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	88.2 % (1571 of 1781)	89.9 % (842 of 937)	85.7 % (593 of 692)	89.5 % (136 of 152)
Backbone	88.3 % (756 of 856)	89.0 % (260 of 292)	87.8 % (374 of 426)	88.4 % (122 of 138)
Sidechain	87.9 % (933 of 1061)	89.8 % (579 of 645)	84.6 % (340 of 402)	100.0 % (14 of 14)
Aromatic	60.5 % (104 of 172)	73.3 % (63 of 86)	46.4 % (39 of 84)	100.0 % (2 of 2)
Methyl	100.0 % (138 of 138)	100.0 % (69 of 69)	100.0 % (69 of 69)

1. HR4394C

MGHHHHHHSH MPDHGDWTYE EQFKQLYELD GDPKRKEFLD DLFSFMQKRG TPVNRIPIMA KQVLDLFMLY VLVTEKGGLV EVINKKLWRE ITKGLNLPTS ITSAAFTLRT QYMKYLYPYE CEKRGLSNPN ELQAAIDSNR REGRR

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1.0 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.92 mM
2	NACL	natural abundance		200 mM

Sample #2

Solvent system 100% D2O, Pressure 1.0 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
3	entity	[U-100% 13C; U-100% 15N]		0.92 mM
4	NACL	natural abundance		200 mM

Sample #3

Solvent system 95% H2O/5% D2O, Pressure 1.0 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
5	entity	[U-10% 13C; U-100% 15N]		0.95 mM
6	NACL	natural abundance		200 mM

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: 0.39 ppm, Outliers: 2 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: 0.39 ppm, Outliers: 2 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: 0.08 ppm, Outliers: 1 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: 0.12 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2KK0, Strand ID: A Detail

Release date

2009-08-05

Citation

SOLUTION STRUCTURE OF DEAD RINGER-LIKE PROTEIN 1 (AT-RICH INTERACTIVE DOMAIN-CONTAINING PROTEIN 3A) FROM HOMO SAPIENS, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) TARGET HR4394C
Liu, G., Xiao, R., Montelione, G.T.
Not known

Related entities 1. DEAD RINGER-LIKE PROTEIN 1, : 1 : 2 : 47 entities Detail

Interaction partners 1. DEAD RINGER-LIKE PROTEIN 1, : 12 interactors Detail

More details for 12 interactors identified by 5 citations

Experiments performed 12 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1.0 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.92 mM
2	NACL	natural abundance		200 mM

2 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1.0 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
5	entity	[U-10% 13C; U-100% 15N]		0.95 mM
6	NACL	natural abundance		200 mM

3 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1.0 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
5	entity	[U-10% 13C; U-100% 15N]		0.95 mM
6	NACL	natural abundance		200 mM

4 3D CBCA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1.0 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.92 mM
2	NACL	natural abundance		200 mM

5 3D HNCO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1.0 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.92 mM
2	NACL	natural abundance		200 mM

6 3D HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1.0 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.92 mM
2	NACL	natural abundance		200 mM

7 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1.0 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
3	entity	[U-100% 13C; U-100% 15N]		0.92 mM
4	NACL	natural abundance		200 mM

8 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1.0 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
3	entity	[U-100% 13C; U-100% 15N]		0.92 mM
4	NACL	natural abundance		200 mM

9 3D HBHA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1.0 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.92 mM
2	NACL	natural abundance		200 mM

10 3D H(CCO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1.0 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.92 mM
2	NACL	natural abundance		200 mM

11 3D HCCH-COSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1.0 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
3	entity	[U-100% 13C; U-100% 15N]		0.92 mM
4	NACL	natural abundance		200 mM

12 3D 1H-13C-15N simutaneous NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1.0 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.92 mM
2	NACL	natural abundance		200 mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_16348_2kk0.nef
Input source #2: Coordindates	2kk0.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
MGHHHHHHSHMPDHGDWTYEEQFKQLYELDGDPKRKEFLDDLFSFMQKRGTPVNRIPIMAKQVLDLFMLYVLVTEKGGLVEVINKKLWREITKGLNLPTS
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MGHHHHHHSHMPDHGDWTYEEQFKQLYELDGDPKRKEFLDDLFSFMQKRGTPVNRIPIMAKQVLDLFMLYVLVTEKGGLVEVINKKLWREITKGLNLPTS

-------110-------120-------130-------140-----
ITSAAFTLRTQYMKYLYPYECEKRGLSNPNELQAAIDSNRREGRR
|||||||||||||||||||||||||||||||||||||||||||||
ITSAAFTLRTQYMKYLYPYECEKRGLSNPNELQAAIDSNRREGRR

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	145	0	0	100.0

Content subtype: combined_16348_2kk0.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1563		92.4 (chain: A, length: 145)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	5254 (1)	noe	91.7 (chain: A, length: 145)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	84 (1)	hbond	46.2 (chain: A, length: 145)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	185 (185)	.	81.4 (chain: A, length: 145)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 145, Sequence coverage: 92.4%
- Total number of assignments
  - ¹H chemical shifts: 842
  - ¹³C chemical shifts: 587
  - ¹⁵N chemical shifts: 134
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
74	THR	HG1	4.17
92	THR	HG1	5.02
110	THR	HG1	4.64

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	937	839	89.5
¹³C chemical shifts	692	587	84.8
¹⁵N chemical shifts	162	134	82.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	292	260	89.0
¹³C chemical shifts	290	247	85.2
¹⁵N chemical shifts	138	119	86.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	645	579	89.8
¹³C chemical shifts	402	340	84.6
¹⁵N chemical shifts	24	15	62.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	75	74	98.7
¹³C chemical shifts	75	74	98.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	86	68	79.1
¹³C chemical shifts	84	42	50.0
¹⁵N chemical shifts	2	2	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: 145, Sequence coverage: 91.7%
- Total number of restraints: 5254
- Weight of restraints: 1.0 (5254)
- Potential type of restraints: square-well-parabolic (5254)
- Range of distance target values: 2.17, 4.81 (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: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 145, Sequence coverage: 46.2%
  - Total number of restraints: 84
  - Weight of restraints: 1.0 (84)
  - Potential type of restraints: square-well-parabolic (84)
  - Range of distance target values: 2.05, 2.62 (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: 145, Sequence coverage: 81.4%
- Total number of restraints: 185
- Total number of restraints per polymer type: 185
- Weight of restraints: 1.0 (185)
- Potential type of restraints: square-well-parabolic (185)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords ARID, AT-rich interaction domain, Dead Ringer, NMR, nesg

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Found 1 Document (1.147 seconds)

BMRB: 16348

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. DEAD RINGER-LIKE PROTEIN 1, : 1 : 2 : 47 entities Detail

Interaction partners 1. DEAD RINGER-LIKE PROTEIN 1, : 12 interactors Detail

Experiments performed 12 experiments Detail

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NMR combined restraints 5 contents Detail