BMRBj - BMREntryMaster

Found 1 Document (0.672 seconds)

BMRB: 17484

2L9R

Solution NMR Structure of Homeobox domain of Homeobox protein Nkx-3.1 from homo sapiens, Northeast Structural Genomics Consortium Target HR6470A

Authors

Liu, G., Xiao, R., Lee, H., Hamilton, K., Ciccosanti, C., Wang, H.B., Acton, T.B., Everett, J.K., Huang, Y.J., Montelione, G.T.

Assembly

HR6470A

Entity

1. HR6470A (polymer, Thiol state: not present), 69 monomers, 8347.433 Da Detail

MGHHHHHHSH MSHTQVIELE RKFSHQKYLS APERAHLAKN LKLTETQVKI WFQNRRYKTK RKQLSSELG

Formula weight

8347.433 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

distance geometry, torsion angle dynamics, molecular dynamics

Data set

assigned_chemical_shifts, RDCs

Chem. Shift Complete

Sequence coverage: 89.9 %, Completeness: 87.8 %, Completeness (bb): 87.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	87.8 % (763 of 869)	88.5 % (407 of 460)	87.1 % (290 of 333)	86.8 % (66 of 76)
Backbone	87.4 % (360 of 412)	88.5 % (123 of 139)	87.3 % (179 of 205)	85.3 % (58 of 68)
Sidechain	88.4 % (463 of 524)	88.5 % (284 of 321)	87.7 % (171 of 195)	100.0 % (8 of 8)
Aromatic	68.2 % (60 of 88)	68.2 % (30 of 44)	67.4 % (29 of 43)	100.0 % (1 of 1)
Methyl	100.0 % (58 of 58)	100.0 % (29 of 29)	100.0 % (29 of 29)

1. HR6470A

MGHHHHHHSH MSHTQVIELE RKFSHQKYLS APERAHLAKN LKLTETQVKI WFQNRRYKTK RKQLSSELG

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.69 mM [U-100% 13C; U-100% 15N] HR6470A, 90% H2O/10% D2O; NMR buffer 6.5 -- 0.02% NaN3, 10mM DTT, 5mM CaCL2, 100mM NaCL, 1x Proteinase Inhibitors, 20mM MES pH 6.5, 10% D2O, 50uM DSS

#	Name	Isotope labeling	Concentration
1	HR6470A	[U-100% 13C; U-100% 15N]	0.69 mM
2	NaN3	natural abundance	0.02 %
3	DTT	natural abundance	10 mM
4	CaCl2	natural abundance	5 mM
5	MES	natural abundance	20 mM
6	NaCl	natural abundance	100 mM
7	DSS	natural abundance	50 uM
8	H2O	natural abundance	90 %
9	D2O	natural abundance	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.65 mM [U-5% 13C; U-100% 15N] HR6470A, 90% H2O/10% D2O; NMR buffer 6.5 -- 0.02% NaN3, 10mM DTT, 5mM CaCL2, 100mM NaCL, 1x Proteinase Inhibitors, 20mM MES pH 6.5, 10% D2O, 50uM DSS

#	Name	Isotope labeling	Concentration
10	HR6470A	[U-5% 13C; U-100% 15N]	0.65 mM
11	NaN3	natural abundance	0.02 %
12	DTT	natural abundance	10 mM
13	CaCl2	natural abundance	5 mM
14	MES	natural abundance	20 mM
15	NaCl	natural abundance	100 mM
16	DSS	natural abundance	50 uM
17	H2O	natural abundance	90 %
18	D2O	natural abundance	10 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: -0.08 ppm, Outliers: 2 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: -0.08 ppm, Outliers: 2 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: 0.05 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: -0.29 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2L9R, Strand ID: A Detail

RDC

91 RDC values in 2 lists
Field strength (¹H) 0.0 MHz, Pressure 1 atm, Temperature 298 K, pH 6.5 Detail

Release date

2012-06-04

Related entities 1. HR6470A, : 1 : 155 entities Detail

Interaction partners 1. HR6470A, : 3 interactors Detail

More details for 3 interactors identified by 2 citations

Experiments performed 7 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.69 mM [U-100% 13C; U-100% 15N] HR6470A, 90% H2O/10% D2O; NMR buffer 6.5 -- 0.02% NaN3, 10mM DTT, 5mM CaCL2, 100mM NaCL, 1x Proteinase Inhibitors, 20mM MES pH 6.5, 10% D2O, 50uM DSS

#	Name	Isotope labeling	Concentration
1	HR6470A	[U-100% 13C; U-100% 15N]	0.69 mM
2	NaN3	natural abundance	0.02 %
3	DTT	natural abundance	10 mM
4	CaCl2	natural abundance	5 mM
5	MES	natural abundance	20 mM
6	NaCl	natural abundance	100 mM
7	DSS	natural abundance	50 uM
8	H2O	natural abundance	90 %
9	D2O	natural abundance	10 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.65 mM [U-5% 13C; U-100% 15N] HR6470A, 90% H2O/10% D2O; NMR buffer 6.5 -- 0.02% NaN3, 10mM DTT, 5mM CaCL2, 100mM NaCL, 1x Proteinase Inhibitors, 20mM MES pH 6.5, 10% D2O, 50uM DSS

#	Name	Isotope labeling	Concentration
10	HR6470A	[U-5% 13C; U-100% 15N]	0.65 mM
11	NaN3	natural abundance	0.02 %
12	DTT	natural abundance	10 mM
13	CaCl2	natural abundance	5 mM
14	MES	natural abundance	20 mM
15	NaCl	natural abundance	100 mM
16	DSS	natural abundance	50 uM
17	H2O	natural abundance	90 %
18	D2O	natural abundance	10 %

3 3D HNCO

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	HR6470A	[U-100% 13C; U-100% 15N]	0.69 mM
2	NaN3	natural abundance	0.02 %
3	DTT	natural abundance	10 mM
4	CaCl2	natural abundance	5 mM
5	MES	natural abundance	20 mM
6	NaCl	natural abundance	100 mM
7	DSS	natural abundance	50 uM
8	H2O	natural abundance	90 %
9	D2O	natural abundance	10 %

4 3D CBCA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	HR6470A	[U-100% 13C; U-100% 15N]	0.69 mM
2	NaN3	natural abundance	0.02 %
3	DTT	natural abundance	10 mM
4	CaCl2	natural abundance	5 mM
5	MES	natural abundance	20 mM
6	NaCl	natural abundance	100 mM
7	DSS	natural abundance	50 uM
8	H2O	natural abundance	90 %
9	D2O	natural abundance	10 %

5 3D HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	HR6470A	[U-100% 13C; U-100% 15N]	0.69 mM
2	NaN3	natural abundance	0.02 %
3	DTT	natural abundance	10 mM
4	CaCl2	natural abundance	5 mM
5	MES	natural abundance	20 mM
6	NaCl	natural abundance	100 mM
7	DSS	natural abundance	50 uM
8	H2O	natural abundance	90 %
9	D2O	natural abundance	10 %

6 3D 1H-13C arom NOESY

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	HR6470A	[U-100% 13C; U-100% 15N]	0.69 mM
2	NaN3	natural abundance	0.02 %
3	DTT	natural abundance	10 mM
4	CaCl2	natural abundance	5 mM
5	MES	natural abundance	20 mM
6	NaCl	natural abundance	100 mM
7	DSS	natural abundance	50 uM
8	H2O	natural abundance	90 %
9	D2O	natural abundance	10 %

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

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	HR6470A	[U-100% 13C; U-100% 15N]	0.69 mM
2	NaN3	natural abundance	0.02 %
3	DTT	natural abundance	10 mM
4	CaCl2	natural abundance	5 mM
5	MES	natural abundance	20 mM
6	NaCl	natural abundance	100 mM
7	DSS	natural abundance	50 uM
8	H2O	natural abundance	90 %
9	D2O	natural abundance	10 %

NMR combined restraints 8 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_17484_2l9r.nef
Input source #2: Coordindates	2l9r.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---------
MGHHHHHHSHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQLSSELG
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MGHHHHHHSHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQLSSELG

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	69	0	0	100.0

Content subtype: combined_17484_2l9r.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	748		87.0 (chain: A, length: 69)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	1828 (1)	noe	87.0 (chain: A, length: 69)
2	Distance restraints	CNS/XPLOR_distance_constraints_5	OK	38 (1)	hbond	44.9 (chain: A, length: 69)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	70 (70)	.	59.4 (chain: A, length: 69)
2	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	70 (70)	.	59.4 (chain: A, length: 69)
1	RDC restraints	DYANA/DIANA_dipolar_coupling_7	OK	36 (36)	.	52.2 (chain: A, length: 69)
2	RDC restraints	DYANA/DIANA_dipolar_coupling_9	OK	37 (37)	.	53.6 (chain: A, length: 69)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 69, Sequence coverage: 87.0%
- Total number of assignments
  - ¹H chemical shifts: 398
  - ¹³C chemical shifts: 285
  - ¹⁵N chemical shifts: 65
- Completeness of assignments
  - Entity_assemble_ID: A
- 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	460	398	86.5
¹³C chemical shifts	333	285	85.6
¹⁵N chemical shifts	81	65	80.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	139	118	84.9
¹³C chemical shifts	138	117	84.8
¹⁵N chemical shifts	68	57	83.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	321	280	87.2
¹³C chemical shifts	195	168	86.2
¹⁵N chemical shifts	13	8	61.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	31	29	93.5
¹³C chemical shifts	31	29	93.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	44	28	63.6
¹³C chemical shifts	43	27	62.8
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: 69, Sequence coverage: 87.0%
- Total number of restraints: 1826
- Weight of restraints: 1.0 (1826)
- Potential type of restraints: square-well-parabolic (1826)
- Range of distance target values: 2.32, 4.2 (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_5
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 69, Sequence coverage: 44.9%
  - Total number of restraints: 38
  - Weight of restraints: 1.0 (38)
  - Potential type of restraints: square-well-parabolic (38)
  - Range of distance target values: 1.94, 2.92 (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: 69, Sequence coverage: 59.4%
- Total number of restraints: 70
- Total number of restraints per polymer type: 70
- Weight of restraints: 1.0 (70)
- Potential type of restraints: square-well-parabolic (70)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
- Saveframe: CNS/XPLOR_dihedral_4
  - Status: OK
  - Experiment type: .
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 69, Sequence coverage: 59.4%
  - Total number of restraints: 70
  - Total number of restraints per polymer type: 70
  - Weight of restraints: 1.0 (70)
  - Potential type of restraints: square-well-parabolic (70)
  - Plot of Phi-Psi angle restraints
  - Dihedral angle restraints per residue
    - Chain_ID: A

RDC restraints

Saveframe: DYANA/DIANA_dipolar_coupling_7

Status: OK
Experiment type: .

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 69, Sequence coverage: 52.2%

--------10--------20--------30--------40--------50--------60---------
MGHHHHHHSHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQLSSELG
          || |||  ||| ||| | ||| |||  ||||||||| | ||| ||| ||          
..........MS.TQV..LER.FSH.K.LSA.ERA..AKNLKLTET.V.IWF.NRR.KT          
--------10--------20--------30--------40--------50---------

Total number of restraints: 36
Potential type of restraints: undefined (36)
Range of observed RDC values: 100.0, -100.0 (Hz)
RDC restraints per residue
- Chain_ID: A
  None

Saveframe: DYANA/DIANA_dipolar_coupling_9

Status: OK
Experiment type: .

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 69, Sequence coverage: 53.6%

--------10--------20--------30--------40--------50--------60---------
MGHHHHHHSHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQLSSELG
           | |||| ||| |||||  || || | ||||||||| |||||| || ||          
...........S.TQVI.LER.FSHQK..SA.ER.H.AKNLKLTET.VKIWFQ.RR.KT          
--------10--------20--------30--------40--------50---------

Total number of restraints: 37
Potential type of restraints: undefined (37)
Range of observed RDC values: 100.0, -100.0 (Hz)
RDC restraints per residue
- Chain_ID: A
  None

Keywords CASP/CASD/method development target, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG), Protein NMR, PSI-biology, Structural Genomics, Target HR6470A, transcription factor

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 (0.672 seconds)

BMRB: 17484

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. HR6470A, : 1 : 155 entities Detail

Interaction partners 1. HR6470A, : 3 interactors Detail

Experiments performed 7 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 8 contents Detail