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BMRB: 18511

2LU7

Solution NMR Structure of Ig like domain (1277-1357) of Obscurin-like protein 1 from Homo sapiens, Northeast Structural Genomics Consortium (NESG) Target HR8578D

Authors

Pulavarti, S., Eletsky, A., Satyamoorthy, B., Sukumaran, D.K., Lee, D., Kohan, E., Janjua, H., Xiao, R., Acton, T.B., Everett, J.K., Montelione, G.T., Szyperski, T.

Assembly

HR8578D

Entity

1. HR8578D (polymer, Thiol state: all free), 84 monomers, 9101.055 Da Detail

SHMTRVRSTP GGDLELVVHL SGPGGPVRWY KDGERLASQG RVQLEQAGAR QVLRVQGARS GDAGEYLCDA PQDSRIFLVS VEEP

Formula weight

9101.055 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 96.4 %, Completeness: 94.2 %, Completeness (bb): 93.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	94.2 % (870 of 924)	94.6 % (457 of 483)	94.1 % (334 of 355)	91.9 % (79 of 86)
Backbone	93.7 % (463 of 494)	93.7 % (163 of 174)	94.6 % (228 of 241)	91.1 % (72 of 79)
Sidechain	94.6 % (476 of 503)	95.1 % (294 of 309)	93.6 % (175 of 187)	100.0 % (7 of 7)
Aromatic	78.3 % (36 of 46)	91.3 % (21 of 23)	63.6 % (14 of 22)	100.0 % (1 of 1)
Methyl	100.0 % (88 of 88)	100.0 % (44 of 44)	100.0 % (44 of 44)

1. HR8578D

SHMTRVRSTP GGDLELVVHL SGPGGPVRWY KDGERLASQG RVQLEQAGAR QVLRVQGARS GDAGEYLCDA PQDSRIFLVS VEEP

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.56 mM HR8578D.005, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR8578D.005	[U-100% 13C; U-100% 15N]	0.56 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	H20	natural abundance	90 %
7	D20	natural abundance	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.52 mM HR8578D.006, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
8	HR8578D.006	[U-5% 13C; U-100% 15N]	0.52 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	H20	natural abundance	90 %
14	D20	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: 0.14 ppm, Outliers: 1 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: 0.14 ppm, Outliers: 1 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: -0.12 ppm, Outliers: 3 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: 0.82 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2LU7, Strand ID: A Detail

Release date

2012-08-20

Related entities 1. HR8578D, : 1 : 2 : 222 entities Detail

Interaction partners 1. HR8578D, : 16 interactors Detail

More details for 16 interactors identified by 11 citations

Experiments performed 18 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 750 MHz NMR facility at SUNY Buffalo

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.56 mM HR8578D.005, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR8578D.005	[U-100% 13C; U-100% 15N]	0.56 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	H20	natural abundance	90 %
7	D20	natural abundance	10 %

2 2D 1H-13C HSQC aliphatic

Instrument

Varian INOVA - 600 MHz NMR facility at SUNY Buffalo

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.56 mM HR8578D.005, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR8578D.005	[U-100% 13C; U-100% 15N]	0.56 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	H20	natural abundance	90 %
7	D20	natural abundance	10 %

3 3D HNCO

Instrument

Varian INOVA - 600 MHz NMR facility at SUNY Buffalo

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.56 mM HR8578D.005, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR8578D.005	[U-100% 13C; U-100% 15N]	0.56 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	H20	natural abundance	90 %
7	D20	natural abundance	10 %

4 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz NMR facility at SUNY Buffalo

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.56 mM HR8578D.005, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR8578D.005	[U-100% 13C; U-100% 15N]	0.56 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	H20	natural abundance	90 %
7	D20	natural abundance	10 %

5 3D HNCACB

Instrument

Varian INOVA - 600 MHz NMR facility at SUNY Buffalo

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.56 mM HR8578D.005, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR8578D.005	[U-100% 13C; U-100% 15N]	0.56 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	H20	natural abundance	90 %
7	D20	natural abundance	10 %

6 3D HBHA(CO)NH

Instrument

Varian INOVA - 600 MHz NMR facility at SUNY Buffalo

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.56 mM HR8578D.005, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR8578D.005	[U-100% 13C; U-100% 15N]	0.56 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	H20	natural abundance	90 %
7	D20	natural abundance	10 %

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

Instrument

Varian INOVA - 750 MHz NMR facility at SUNY Buffalo

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.56 mM HR8578D.005, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR8578D.005	[U-100% 13C; U-100% 15N]	0.56 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	H20	natural abundance	90 %
7	D20	natural abundance	10 %

8 2D 1H-13C HSQC (CT-28 ms) aliphatic

Instrument

Varian INOVA - 600 MHz NMR facility at SUNY Buffalo

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.52 mM HR8578D.006, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
8	HR8578D.006	[U-5% 13C; U-100% 15N]	0.52 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	H20	natural abundance	90 %
14	D20	natural abundance	10 %

9 2D 1H-13C HSQC aromatic

Instrument

Varian INOVA - 750 MHz NMR facility at SUNY Buffalo

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.56 mM HR8578D.005, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR8578D.005	[U-100% 13C; U-100% 15N]	0.56 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	H20	natural abundance	90 %
7	D20	natural abundance	10 %

10 2D 1H-13C HSQC (CT-16 ms) aromatic

Instrument

Varian INOVA - 750 MHz NMR facility at SUNY Buffalo

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.56 mM HR8578D.005, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR8578D.005	[U-100% 13C; U-100% 15N]	0.56 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	H20	natural abundance	90 %
7	D20	natural abundance	10 %

11 2D 1H-13C HSQC (CT-27 ms) aliphatic

Instrument

Varian INOVA - 750 MHz NMR facility at SUNY Buffalo

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.56 mM HR8578D.005, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR8578D.005	[U-100% 13C; U-100% 15N]	0.56 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	H20	natural abundance	90 %
7	D20	natural abundance	10 %

12 3D C(CO)NH-TOCSY

Instrument

Varian INOVA - 750 MHz NMR facility at SUNY Buffalo

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.56 mM HR8578D.005, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR8578D.005	[U-100% 13C; U-100% 15N]	0.56 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	H20	natural abundance	90 %
7	D20	natural abundance	10 %

13 3D H(CCO)NH-TOCSY

Instrument

Varian INOVA - 750 MHz NMR facility at SUNY Buffalo

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.56 mM HR8578D.005, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR8578D.005	[U-100% 13C; U-100% 15N]	0.56 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	H20	natural abundance	90 %
7	D20	natural abundance	10 %

14 3D HCCH-TOCSY

Instrument

Varian INOVA - 750 MHz NMR facility at SUNY Buffalo

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.56 mM HR8578D.005, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR8578D.005	[U-100% 13C; U-100% 15N]	0.56 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	H20	natural abundance	90 %
7	D20	natural abundance	10 %

15 3D-HCCH-COSY-ali

Instrument

Varian INOVA - 750 MHz NMR facility at SUNY Buffalo

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.56 mM HR8578D.005, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR8578D.005	[U-100% 13C; U-100% 15N]	0.56 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	H20	natural abundance	90 %
7	D20	natural abundance	10 %

16 3D HCCH-COSY-aro

Instrument

Varian INOVA - 750 MHz NMR facility at SUNY Buffalo

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.56 mM HR8578D.005, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR8578D.005	[U-100% 13C; U-100% 15N]	0.56 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	H20	natural abundance	90 %
7	D20	natural abundance	10 %

17 2D 1H-13C HSQC (CT-56 ms) aliphatic

Instrument

Varian INOVA - 600 MHz NMR facility at SUNY Buffalo

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.52 mM HR8578D.006, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
8	HR8578D.006	[U-5% 13C; U-100% 15N]	0.52 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	H20	natural abundance	90 %
14	D20	natural abundance	10 %

18 3D HN(CA)CO

Instrument

Varian INOVA - 600 MHz NMR facility at SUNY Buffalo

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.56 mM HR8578D.005, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR8578D.005	[U-100% 13C; U-100% 15N]	0.56 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	H20	natural abundance	90 %
7	D20	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_18511_2lu7.nef
Input source #2: Coordindates	2lu7.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

-0--------10--------20--------30--------40--------50--------60--------70--------80--
SHMTRVRSTPGGDLELVVHLSGPGGPVRWYKDGERLASQGRVQLEQAGARQVLRVQGARSGDAGEYLCDAPQDSRIFLVSVEEP
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
SHMTRVRSTPGGDLELVVHLSGPGGPVRWYKDGERLASQGRVQLEQAGARQVLRVQGARSGDAGEYLCDAPQDSRIFLVSVEEP
--------10--------20--------30--------40--------50--------60--------70--------80----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	84	0	0	100.0

Content subtype: combined_18511_2lu7.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	866		95.2 (chain: A, length: 84)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	1405 (1)	noe	92.9 (chain: A, length: 84)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	64 (64)	.	57.1 (chain: A, length: 84)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 84, Sequence coverage: 95.2%
- Total number of assignments
  - ¹H chemical shifts: 453
  - ¹³C chemical shifts: 334
  - ¹⁵N chemical shifts: 79
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	483	453	93.8
¹³C chemical shifts	355	334	94.1
¹⁵N chemical shifts	95	79	83.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	174	159	91.4
¹³C chemical shifts	168	158	94.0
¹⁵N chemical shifts	79	70	88.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	309	294	95.1
¹³C chemical shifts	187	176	94.1
¹⁵N chemical shifts	16	9	56.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	45	45	100.0
¹³C chemical shifts	45	45	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	23	21	91.3
¹³C chemical shifts	22	14	63.6
¹⁵N chemical shifts	1	1	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 84, Sequence coverage: 92.9%
- Total number of restraints: 1403
- Weight of restraints: 1.0 (1403)
- Potential type of restraints: square-well-parabolic (1403)
- Range of distance target values: 1.59, 3.15 (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_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 84, Sequence coverage: 57.1%
- Total number of restraints: 64
- Total number of restraints per polymer type: 64
- Weight of restraints: 1.0 (64)
- Potential type of restraints: square-well-parabolic (64)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG), Protein NMR, Protein Structure Initiative, PSI-Biology, Structural Genomics, Target HR8578D

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Found 1 Document (0.975 seconds)

BMRB: 18511

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. HR8578D, : 1 : 2 : 222 entities Detail

Interaction partners 1. HR8578D, : 16 interactors Detail

Experiments performed 18 experiments Detail

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NMR combined restraints 4 contents Detail