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Found 1 Document (1.022 seconds)

BMRB: 18489

2LTM

Solution NMR Structure of NFU1 Iron-Sulfur Cluster Scaffold Homolog from Homo sapiens, Northeast Structural Genomics Consortium (NESG) Target HR2876B

Authors

Liu, G., Xiao, R., Janjua, H., Hamilton, K., Shastry, R., Kohan, E., Acton, T.B., Everett, J.K., Lee, H., Huang, Y.J., Montelione, G.T., Northeast Structural Genomics Consortium, N.

Assembly

HR2876B

Entity

1. HR2876B (polymer, Thiol state: all free), 107 monomers, 12185.73 Da Detail

MGHHHHHHSH MFIQTQDTPN PNSLKFIPGK PVLETRTMDF PTPAAAFRSP LARQLFRIEG VKSVFFGPDS ITVTKENEEL DWNLLKPDIY ATIMDFFASG LPLVTEE

Formula weight

12185.73 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

distance geometry, simulated annealing, torsion angle dynamics, molecular dynamics

Data set

RDCs, assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 91.6 %, Completeness: 90.0 %, Completeness (bb): 87.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	90.0 % (1148 of 1276)	90.9 % (602 of 662)	89.2 % (454 of 509)	87.6 % (92 of 105)
Backbone	87.9 % (547 of 622)	89.0 % (186 of 209)	87.7 % (277 of 316)	86.6 % (84 of 97)
Sidechain	91.9 % (695 of 756)	91.8 % (416 of 453)	91.9 % (271 of 295)	100.0 % (8 of 8)
Aromatic	79.7 % (110 of 138)	79.7 % (55 of 69)	79.4 % (54 of 68)	100.0 % (1 of 1)
Methyl	100.0 % (110 of 110)	100.0 % (55 of 55)	100.0 % (55 of 55)

1. HR2876B

MGHHHHHHSH MFIQTQDTPN PNSLKFIPGK PVLETRTMDF PTPAAAFRSP LARQLFRIEG VKSVFFGPDS ITVTKENEEL DWNLLKPDIY ATIMDFFASG LPLVTEE

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.896 mM HR2876B.035, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR2876B.035	[U-100% 13C; U-100% 15N]	0.896 mM
2	NaCl	natural abundance	100 mM
3	DTT	natural abundance	5 mM
4	NaN3	natural abundance	0.02 %
5	Tris-HCl pH 7.5	natural abundance	10 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.92 mM HR2876B.037, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
8	HR2876B.037	[U-5% 13C; U-100% 15N]	0.92 mM
9	NaCl	natural abundance	100 mM
10	DTT	natural abundance	5 mM
11	NaN3	natural abundance	0.02 %
12	Tris-HCl pH 7.5	natural abundance	10 mM
13	H2O	natural abundance	90 %
14	D2O	natural abundance	10 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.92 mM HR2876B.039, 90% H2O/10% D2O, in alignment media : peg or phage

#	Name	Isotope labeling	Concentration
15	HR2876B.039	[U-5% 13C; U-100% 15N]	0.92 mM
16	NaCl	natural abundance	100 mM
17	DTT	natural abundance	5 mM
18	NaN3	natural abundance	0.02 %
19	Tris-HCl pH 7.5	natural abundance	10 mM
20	H2O	natural abundance	90 %
21	D2O	natural abundance	10 %

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: 0.06 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: 0.06 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: -0.04 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: 0.72 ppm, Outliers: 2 Detail

Protein Blocks Logo

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

RDC

147 RDC values in 2 lists
Field strength (¹H) 599.520 MHz, Pressure 1 atm, Temperature 298 K, pH 7.5 Detail

Release date

2012-07-22

Related entities 1. HR2876B, : 1 : 3 : 36 entities Detail

Interaction partners 1. HR2876B, : 15 interactors Detail

More details for 15 interactors identified by 8 citations

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz at Rutgers

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.896 mM HR2876B.035, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR2876B.035	[U-100% 13C; U-100% 15N]	0.896 mM
2	NaCl	natural abundance	100 mM
3	DTT	natural abundance	5 mM
4	NaN3	natural abundance	0.02 %
5	Tris-HCl pH 7.5	natural abundance	10 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 800 MHz at Rutgers

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.896 mM HR2876B.035, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR2876B.035	[U-100% 13C; U-100% 15N]	0.896 mM
2	NaCl	natural abundance	100 mM
3	DTT	natural abundance	5 mM
4	NaN3	natural abundance	0.02 %
5	Tris-HCl pH 7.5	natural abundance	10 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

3 3D HNCO

Instrument

Bruker Avance - 800 MHz at Rutgers

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.896 mM HR2876B.035, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR2876B.035	[U-100% 13C; U-100% 15N]	0.896 mM
2	NaCl	natural abundance	100 mM
3	DTT	natural abundance	5 mM
4	NaN3	natural abundance	0.02 %
5	Tris-HCl pH 7.5	natural abundance	10 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

4 3D CBCA(CO)NH

Instrument

Bruker Avance - 800 MHz at Rutgers

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.896 mM HR2876B.035, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR2876B.035	[U-100% 13C; U-100% 15N]	0.896 mM
2	NaCl	natural abundance	100 mM
3	DTT	natural abundance	5 mM
4	NaN3	natural abundance	0.02 %
5	Tris-HCl pH 7.5	natural abundance	10 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

5 3D HNCACB

Instrument

Bruker Avance - 800 MHz at Rutgers

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.896 mM HR2876B.035, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR2876B.035	[U-100% 13C; U-100% 15N]	0.896 mM
2	NaCl	natural abundance	100 mM
3	DTT	natural abundance	5 mM
4	NaN3	natural abundance	0.02 %
5	Tris-HCl pH 7.5	natural abundance	10 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

6 3D 1H-13C arom NOESY

Instrument

Bruker Avance - 800 MHz at Rutgers

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.896 mM HR2876B.035, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR2876B.035	[U-100% 13C; U-100% 15N]	0.896 mM
2	NaCl	natural abundance	100 mM
3	DTT	natural abundance	5 mM
4	NaN3	natural abundance	0.02 %
5	Tris-HCl pH 7.5	natural abundance	10 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

7 3D simutaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY

Instrument

Bruker Avance - 800 MHz at Rutgers

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.896 mM HR2876B.035, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR2876B.035	[U-100% 13C; U-100% 15N]	0.896 mM
2	NaCl	natural abundance	100 mM
3	DTT	natural abundance	5 mM
4	NaN3	natural abundance	0.02 %
5	Tris-HCl pH 7.5	natural abundance	10 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

8 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz at UGA

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.92 mM HR2876B.039, 90% H2O/10% D2O, in alignment media : peg or phage

#	Name	Isotope labeling	Concentration
15	HR2876B.039	[U-5% 13C; U-100% 15N]	0.92 mM
16	NaCl	natural abundance	100 mM
17	DTT	natural abundance	5 mM
18	NaN3	natural abundance	0.02 %
19	Tris-HCl pH 7.5	natural abundance	10 mM
20	H2O	natural abundance	90 %
21	D2O	natural abundance	10 %

9 2D 1H-13C HSQC aliphatic

Instrument

Varian INOVA - 600 MHz at Rutgers

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.92 mM HR2876B.037, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
8	HR2876B.037	[U-5% 13C; U-100% 15N]	0.92 mM
9	NaCl	natural abundance	100 mM
10	DTT	natural abundance	5 mM
11	NaN3	natural abundance	0.02 %
12	Tris-HCl pH 7.5	natural abundance	10 mM
13	H2O	natural abundance	90 %
14	D2O	natural abundance	10 %

10 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz at Rutgers

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.896 mM HR2876B.035, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR2876B.035	[U-100% 13C; U-100% 15N]	0.896 mM
2	NaCl	natural abundance	100 mM
3	DTT	natural abundance	5 mM
4	NaN3	natural abundance	0.02 %
5	Tris-HCl pH 7.5	natural abundance	10 mM
6	H2O	natural abundance	90 %
7	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	combined_18489_2ltm.nef
Input source #2: Coordindates	2ltm.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
MGHHHHHHSHMFIQTQDTPNPNSLKFIPGKPVLETRTMDFPTPAAAFRSPLARQLFRIEGVKSVFFGPDSITVTKENEELDWNLLKPDIYATIMDFFASG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MGHHHHHHSHMFIQTQDTPNPNSLKFIPGKPVLETRTMDFPTPAAAFRSPLARQLFRIEGVKSVFFGPDSITVTKENEELDWNLLKPDIYATIMDFFASG

-------
LPLVTEE
|||||||
LPLVTEE

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	107	0	0	100.0

Content subtype: combined_18489_2ltm.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1135		90.7 (chain: A, length: 107)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	3973 (1)	noe	90.7 (chain: A, length: 107)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	50 (1)	hbond	33.6 (chain: A, length: 107)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	112 (112)	.	69.2 (chain: A, length: 107)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 107, Sequence coverage: 90.7%
- Total number of assignments
  - ¹H chemical shifts: 597
  - ¹³C chemical shifts: 448
  - ¹⁵N chemical shifts: 90
- Completeness of assignments
  - Entity_assemble_ID: A
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	662	597	90.2
¹³C chemical shifts	509	448	88.0
¹⁵N chemical shifts	109	90	82.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	209	183	87.6
¹³C chemical shifts	214	178	83.2
¹⁵N chemical shifts	97	82	84.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	453	414	91.4
¹³C chemical shifts	295	270	91.5
¹⁵N chemical shifts	12	8	66.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	59	58	98.3
¹³C chemical shifts	59	58	98.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	69	55	79.7
¹³C chemical shifts	68	54	79.4
¹⁵N chemical shifts	1	1	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 107, Sequence coverage: 90.7%
- Total number of restraints: 3968
- Weight of restraints: 1.0 (3968)
- Potential type of restraints: square-well-parabolic (3968)
- Range of distance target values: 2.21, 4.35 (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: 107, Sequence coverage: 33.6%
  - Total number of restraints: 50
  - Weight of restraints: 1.0 (50)
  - Potential type of restraints: square-well-parabolic (50)
  - Range of distance target values: 1.99, 2.99 (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: 107, Sequence coverage: 69.2%
- Total number of restraints: 112
- Total number of restraints per polymer type: 112
- Weight of restraints: 1.0 (112)
- Potential type of restraints: square-well-parabolic (112)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG), PSI-Biology, Protein NMR, Protein Structure Initiative, Structural Genomics, Target HR2876B

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Found 1 Document (1.022 seconds)

BMRB: 18489

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. HR2876B, : 1 : 3 : 36 entities Detail

Interaction partners 1. HR2876B, : 15 interactors Detail

Experiments performed 10 experiments Detail

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NMR combined restraints 5 contents Detail