BMRBj - BMREntryMaster

Found 1 Document (2.169 seconds)

BMRB: 19749

2MK2

Solution NMR structure of N-terminal domain (SH2 domain) of human Inositol polyphosphate phosphatase-like protein 1 (INPPL1) (fragment 20-117), Northeast Structural Genomics Consortium Target HR9134A.

Authors

Yang, Y., Ramelot, T.A., Janjua, H., Xiao, R., Everett, J.K., Montelione, G.T., Kennedy, M.A.

Assembly

N-terminal domain (SH2 domain) of human Inositol polyphosphate phosphatase-like protein 1 (INPPL1)

Entity

1. N-terminal domain (SH2 domain) of human Inositol polyphosphate phosphatase-like protein 1 (INPPL1) (polymer, Thiol state: all free), 109 monomers, 12179.71 Da Detail

MGHHHHHHSH MSWYHRDLSR AAAEELLARA GRDGSFLVRD SESVAGAFAL CVLYQKHVHT YRILPDGEDF LAVQTSQGVP VRRFQTLGEL IGLYAQPNQG LVCALLLPV

Formula weight

12179.71 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 92.7 %, Completeness: 89.2 %, Completeness (bb): 91.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	89.2 % (1110 of 1244)	90.0 % (574 of 638)	87.4 % (431 of 493)	92.9 % (105 of 113)
Backbone	91.2 % (589 of 646)	91.0 % (203 of 223)	90.9 % (289 of 318)	92.4 % (97 of 105)
Sidechain	88.0 % (614 of 698)	89.4 % (371 of 415)	85.5 % (235 of 275)	100.0 % (8 of 8)
Aromatic	58.9 % (73 of 124)	64.5 % (40 of 62)	52.5 % (32 of 61)	100.0 % (1 of 1)
Methyl	100.0 % (132 of 132)	100.0 % (66 of 66)	100.0 % (66 of 66)

1. HR9134A

MGHHHHHHSH MSWYHRDLSR AAAEELLARA GRDGSFLVRD SESVAGAFAL CVLYQKHVHT YRILPDGEDF LAVQTSQGVP VRRFQTLGEL IGLYAQPNQG LVCALLLPV

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.58 mM HR9134A.003, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR9134A	[U-100% 13C; U-100% 15N]	0.58 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.58 mM HR9134A.003, 100% D2O

#	Name	Isotope labeling	Type	Concentration
4	HR9134A	[U-100% 13C; U-100% 15N]		0.58 mM
5	D2O	natural abundance		100 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 1.05 mM HR9134A.003, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
6	HR9134A	[U-5% 13C; U-100% 15N]	1.05 mM
7	H2O	natural abundance	90 %
8	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: -0.26 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: -0.26 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: -0.03 ppm, Outliers: 2 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: 0.24 ppm, Outliers: 4 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2MK2, Strand ID: A Detail

Release date

2014-03-02

Related entities 1. N-terminal domain (SH2 domain) of human Inositol polyphosphate phosphatase-like protein 1 (INPPL1), : 1 : 2 : 233 entities Detail

Interaction partners 1. N-terminal domain (SH2 domain) of human Inositol polyphosphate phosphatase-like protein 1 (INPPL1), : 33 interactors Detail

More details for 33 interactors identified by 18 citations

Experiments performed 17 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 1.05 mM HR9134A.003, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
6	HR9134A	[U-5% 13C; U-100% 15N]	1.05 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	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 1.05 mM HR9134A.003, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
6	HR9134A	[U-5% 13C; U-100% 15N]	1.05 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

3 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 1.05 mM HR9134A.003, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
6	HR9134A	[U-5% 13C; U-100% 15N]	1.05 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	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 1.05 mM HR9134A.003, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
6	HR9134A	[U-5% 13C; U-100% 15N]	1.05 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

5 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 1.05 mM HR9134A.003, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
6	HR9134A	[U-5% 13C; U-100% 15N]	1.05 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

6 3D 1H-13C arom NOESY

Instrument

Bruker Avance - 850 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 1.05 mM HR9134A.003, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
6	HR9134A	[U-5% 13C; U-100% 15N]	1.05 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

7 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 850 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 1.05 mM HR9134A.003, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
6	HR9134A	[U-5% 13C; U-100% 15N]	1.05 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

8 3D 1H-15N NOESY

Instrument

Bruker Avance - 850 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 1.05 mM HR9134A.003, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
6	HR9134A	[U-5% 13C; U-100% 15N]	1.05 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

9 3D HN(CO)CA

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 1.05 mM HR9134A.003, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
6	HR9134A	[U-5% 13C; U-100% 15N]	1.05 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

10 3D HNCA

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 1.05 mM HR9134A.003, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
6	HR9134A	[U-5% 13C; U-100% 15N]	1.05 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

11 2D 1H-15N HSQC NH2 only

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 1.05 mM HR9134A.003, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
6	HR9134A	[U-5% 13C; U-100% 15N]	1.05 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

12 2D 1H-13C HSQC aliphatic

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 1.05 mM HR9134A.003, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
6	HR9134A	[U-5% 13C; U-100% 15N]	1.05 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

13 2D 1H-13C HSQC aromatic

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 1.05 mM HR9134A.003, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
6	HR9134A	[U-5% 13C; U-100% 15N]	1.05 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

14 3D HCCH-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 1.05 mM HR9134A.003, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
6	HR9134A	[U-5% 13C; U-100% 15N]	1.05 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

15 3D HCCH-COSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.58 mM HR9134A.003, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR9134A	[U-100% 13C; U-100% 15N]	0.58 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

16 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 0.58 mM HR9134A.003, 100% D2O

#	Name	Isotope labeling	Type	Concentration
4	HR9134A	[U-100% 13C; U-100% 15N]		0.58 mM
5	D2O	natural abundance		100 %

17 2D 1H-15N HSQC histidine

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 1.05 mM HR9134A.003, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
6	HR9134A	[U-5% 13C; U-100% 15N]	1.05 mM
7	H2O	natural abundance	90 %
8	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_19749_2mk2.nef
Input source #2: Coordindates	2mk2.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
MGHHHHHHSHMSWYHRDLSRAAAEELLARAGRDGSFLVRDSESVAGAFALCVLYQKHVHTYRILPDGEDFLAVQTSQGVPVRRFQTLGELIGLYAQPNQG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MGHHHHHHSHMSWYHRDLSRAAAEELLARAGRDGSFLVRDSESVAGAFALCVLYQKHVHTYRILPDGEDFLAVQTSQGVPVRRFQTLGELIGLYAQPNQG

---------
LVCALLLPV
|||||||||
LVCALLLPV

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	109	0	0	100.0

Content subtype: combined_19749_2mk2.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1111		91.7 (chain: A, length: 109)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	1783 (1)	noe	89.9 (chain: A, length: 109)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	46 (1)	hbond	29.4 (chain: A, length: 109)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	108 (108)	.	64.2 (chain: A, length: 109)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 109, Sequence coverage: 91.7%
- Total number of assignments
  - ¹H chemical shifts: 572
  - ¹³C chemical shifts: 427
  - ¹⁵N chemical shifts: 112
- 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)
12	SER	HG	5.69
15	HIS	ND1	232.4
15	HIS	NE2	188.4
35	SER	HG	5.81
43	SER	HG	5.75
57	HIS	ND1	184.3
57	HIS	NE2	177.4
76	SER	HG	5.57

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	638	568	89.0
¹³C chemical shifts	493	427	86.6
¹⁵N chemical shifts	121	108	89.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	223	202	90.6
¹³C chemical shifts	218	195	89.4
¹⁵N chemical shifts	105	95	90.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	415	366	88.2
¹³C chemical shifts	275	232	84.4
¹⁵N chemical shifts	16	13	81.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	68	66	97.1
¹³C chemical shifts	68	66	97.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	62	39	62.9
¹³C chemical shifts	61	31	50.8
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: 109, Sequence coverage: 89.9%
- Total number of restraints: 1781
- Weight of restraints: 1.0 (1781)
- Potential type of restraints: square-well-parabolic (1781)
- Range of distance target values: 2.25, 3.9 (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: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 109, Sequence coverage: 29.4%
  - Total number of restraints: 46
  - Weight of restraints: 1.0 (46)
  - Potential type of restraints: square-well-parabolic (46)
  - Range of distance target values: 2.0, 3.0 (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: 109, Sequence coverage: 64.2%
- Total number of restraints: 108
- Total number of restraints per polymer type: 108
- Weight of restraints: 1.0 (108)
- Potential type of restraints: square-well-parabolic (108)
- 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 HR9134A

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (2.169 seconds)

BMRB: 19749

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. N-terminal domain (SH2 domain) of human Inositol polyphosphate phosphatase-like protein 1 (INPPL1), : 1 : 2 : 233 entities Detail

Interaction partners 1. N-terminal domain (SH2 domain) of human Inositol polyphosphate phosphatase-like protein 1 (INPPL1), : 33 interactors Detail

Experiments performed 17 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail