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BMRB: 18048

2LLH

NPM1_C70

Authors

Banci, L., Bertini, I., Brunori, M., Di Matteo, A., Federici, L., Gallo, A., Lo Sterzo, C., Mori, M.

Assembly

NPM1 C70

Entity

1. NPM1 C70 (polymer, Thiol state: all free), 70 monomers, 8087.219 Da Detail

QESFKKQEKT PKTPKGPSSV EDIKAKMQAS IEKGGSLPKV EAKFINYVKN CFRMTDQEAI QDLWQWRKSL

Formula weight

8087.219 Da

Source organism

Exptl. method

Refine. method

molecular dynamics, simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.6 %, Completeness: 70.3 %, Completeness (bb): 96.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	70.3 % (614 of 874)	56.0 % (262 of 468)	84.5 % (279 of 330)	96.1 % (73 of 76)
Backbone	96.4 % (397 of 412)	94.2 % (131 of 139)	97.1 % (201 of 207)	98.5 % (65 of 66)
Sidechain	53.3 % (282 of 529)	39.8 % (131 of 329)	75.3 % (143 of 190)	80.0 % (8 of 10)
Aromatic	11.3 % (7 of 62)	12.9 % (4 of 31)	3.4 % (1 of 29)	100.0 % (2 of 2)
Methyl	57.4 % (31 of 54)	22.2 % (6 of 27)	92.6 % (25 of 27)

1. entity

QESFKKQEKT PKTPKGPSSV EDIKAKMQAS IEKGGSLPKV EAKFINYVKN CFRMTDQEAI QDLWQWRKSL

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
1	NPM1_C70	[U-15N]		0.5 mM
2	sodium phosphate	natural abundance		20 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
5	NPM1_C70	[U-13C; U-15N]		0.5 mM
6	sodium phosphate	natural abundance		20 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

LACS Plot; CA

Referencing offset: 2.56 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: 2.56 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: 0.12 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: 2.69 ppm, Outliers: 2 Detail

Protein Blocks Logo

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

Release date

2012-06-18

Citation

Structure of nucleophosmin DNA-binding domain and analysis of its complex with a G-quadruplex sequence from the c-MYC promoter
Gallo, A., Lo Sterzo, C., Mori, M., Di Matteo, A., Bertini, I., Banci, L., Brunori, M., Federici, L.
J. Biol. Chem. (2012), 287, 26539-26548, PubMed 22707729 , DOI 10.1074/jbc.M112.371013 , Abstract

Related entities 1. NPM1 C70, : 1 : 6 : 2 : 7 entities Detail

Interaction partners 1. NPM1 C70, : 163 interactors Detail

More details for 163 interactors identified by 74 citations

Experiments performed 12 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
1	NPM1_C70	[U-15N]		0.5 mM
2	sodium phosphate	natural abundance		20 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

2 3D CBCA(CO)NH

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
5	NPM1_C70	[U-13C; U-15N]		0.5 mM
6	sodium phosphate	natural abundance		20 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

3 3D HNCO

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
5	NPM1_C70	[U-13C; U-15N]		0.5 mM
6	sodium phosphate	natural abundance		20 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

4 3D HNCA

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
5	NPM1_C70	[U-13C; U-15N]		0.5 mM
6	sodium phosphate	natural abundance		20 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

5 3D HNCACB

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
5	NPM1_C70	[U-13C; U-15N]		0.5 mM
6	sodium phosphate	natural abundance		20 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

6 3D HBHA(CO)NH

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
5	NPM1_C70	[U-13C; U-15N]		0.5 mM
6	sodium phosphate	natural abundance		20 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

7 3D HN(CO)CA

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
5	NPM1_C70	[U-13C; U-15N]		0.5 mM
6	sodium phosphate	natural abundance		20 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

8 3D HN(CA)CO

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
5	NPM1_C70	[U-13C; U-15N]		0.5 mM
6	sodium phosphate	natural abundance		20 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

9 3D HCCH-TOCSY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
5	NPM1_C70	[U-13C; U-15N]		0.5 mM
6	sodium phosphate	natural abundance		20 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

10 2D 1H-1H NOESY

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
1	NPM1_C70	[U-15N]		0.5 mM
2	sodium phosphate	natural abundance		20 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

11 3D 1H-13C NOESY

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
5	NPM1_C70	[U-13C; U-15N]		0.5 mM
6	sodium phosphate	natural abundance		20 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

12 3D 1H-15N NOESY

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
1	NPM1_C70	[U-15N]		0.5 mM
2	sodium phosphate	natural abundance		20 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18048_2llh.nef
Input source #2: Coordindates	2llh.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
GSHMQESFKKQEKTPKTPKGPSSVEDIKAKMQASIEKGGSLPKVEAKFINYVKNCFRMTDQEAIQDLWQWRKSL
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSHMQESFKKQEKTPKTPKGPSSVEDIKAKMQASIEKGGSLPKVEAKFINYVKNCFRMTDQEAIQDLWQWRKSL
--------10--------20--------30--------40--------50--------60--------70----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	74	0	0	100.0

Content subtype: combined_18048_2llh.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	590		93.2 (chain: A, length: 74)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	979 (1)	noe	93.2 (chain: A, length: 74)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	300 (300)	.	94.6 (chain: A, length: 74)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 74, Sequence coverage: 93.2%
- Total number of assignments
  - ¹H chemical shifts: 241
  - ¹³C chemical shifts: 276
  - ¹⁵N chemical shifts: 73
- 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

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 74, Sequence coverage: 93.2%
- Total number of restraints: 975
- Weight of restraints: 1.0 (975)
- Potential type of restraints: upper-bound-parabolic (975)
- Range of distance target values: 2.0, 5.8 (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

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 74, Sequence coverage: 94.6%
- Total number of restraints: 300
- Total number of restraints per polymer type: 300
- Weight of restraints: 1.0 (300)
- Potential type of restraints: square-well-parabolic (300)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords CHROMOSOMAL REARRANGEMENT, NUCLEAR PROTEIN, PROTO-ONCOGENE