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Found 1 Document (0.847 seconds)

BMRB: 17683

2LDU

Solution NMR Structure of Heat shock factor protein 1 DNA binding domain from homo sapiens, Northeast Structural Genomics Consortium Target HR3023C

Authors

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

Assembly

HR3023C

Entity

1. HR3023C (polymer, Thiol state: all free), 125 monomers, 14377.15 Da Detail

MGHHHHHHSH MAGPSNVPAF LTKLWTLVSD PDTDALICWS PSGNSFHVFD QGQFAKEVLP KYFKHNNMAS FVRQLNMYGF RKVVHIEQGG LVKPERDDTE FQHPCFLRGQ EQLLENIKRK VTSVS

Formula weight

14377.15 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

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

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 92.0 %, Completeness: 90.9 %, Completeness (bb): 90.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	90.9 % (1362 of 1499)	91.2 % (712 of 781)	90.8 % (531 of 585)	89.5 % (119 of 133)
Backbone	90.1 % (663 of 736)	90.0 % (226 of 251)	90.5 % (332 of 367)	89.0 % (105 of 118)
Sidechain	91.8 % (808 of 880)	91.7 % (486 of 530)	91.9 % (308 of 335)	93.3 % (14 of 15)
Aromatic	81.6 % (142 of 174)	83.9 % (73 of 87)	80.0 % (68 of 85)	50.0 % (1 of 2)
Methyl	100.0 % (112 of 112)	100.0 % (56 of 56)	100.0 % (56 of 56)

1. HR3023C

MGHHHHHHSH MAGPSNVPAF LTKLWTLVSD PDTDALICWS PSGNSFHVFD QGQFAKEVLP KYFKHNNMAS FVRQLNMYGF RKVVHIEQGG LVKPERDDTE FQHPCFLRGQ EQLLENIKRK VTSVS

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.51 mM [U-100% 13C; U-100% 15N], 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR3023C	[U-100% 13C; U-100% 15N]	0.51 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 6.5, Details 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
4	HR3023C	[U-100% 13C; U-100% 15N]	0.43 mM
5	NaN3	natural abundance	0.02 %
6	DTT	natural abundance	10 mM
7	CaCL2	natural abundance	5 mM
8	NaCL	natural abundance	100 mM
9	Proteinase Inhibitors	natural abundance	1 na
10	MES	natural abundance	20 mM
11	DSS	natural abundance	50 uM
12	D2O	natural abundance	10 %
13	H2O	natural abundance	90 %

Sample #3

#	Name	Isotope labeling	Concentration
14	HR3023C	[U-100% 13C; U-100% 15N]	0.43 mM
15	NaN3	natural abundance	0.02 %
16	DTT	natural abundance	10 mM
17	CaCL2	natural abundance	5 mM
18	NaCL	natural abundance	100 mM
19	Proteinase Inhibitors	natural abundance	1 na
20	MES	natural abundance	20 mM
21	DSS	natural abundance	50 uM
22	D2O	natural abundance	10 %
23	H2O	natural abundance	90 %

Sample #4

#	Name	Isotope labeling	Concentration
24	HR3023C	[U-100% 13C; U-100% 15N]	0.43 mM
25	NaN3	natural abundance	0.02 %
26	DTT	natural abundance	10 mM
27	CaCL2	natural abundance	5 mM
28	NaCL	natural abundance	100 mM
29	Proteinase Inhibitors	natural abundance	1 na
30	MES	natural abundance	20 mM
31	DSS	natural abundance	50 uM
32	D2O	natural abundance	10 %
33	H2O	natural abundance	90 %

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: -0.06 ppm, Outliers: 1 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: -0.06 ppm, Outliers: 1 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: -0.02 ppm, Outliers: 3 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: 0.31 ppm, Outliers: 2 Detail

Protein Blocks Logo

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

Release date

2011-07-04

Related entities 1. HR3023C, : 1 : 7 : 189 entities Detail

Interaction partners 1. HR3023C, : 3 interactors Detail

More details for 3 interactors identified by 2 citations

Experiments performed 10 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 0.51 mM [U-100% 13C; U-100% 15N], 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR3023C	[U-100% 13C; U-100% 15N]	0.51 mM
2	H2O	natural abundance	90 %
3	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 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
4	HR3023C	[U-100% 13C; U-100% 15N]	0.43 mM
5	NaN3	natural abundance	0.02 %
6	DTT	natural abundance	10 mM
7	CaCL2	natural abundance	5 mM
8	NaCL	natural abundance	100 mM
9	Proteinase Inhibitors	natural abundance	1 na
10	MES	natural abundance	20 mM
11	DSS	natural abundance	50 uM
12	D2O	natural abundance	10 %
13	H2O	natural abundance	90 %

3 3D HNCO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.51 mM [U-100% 13C; U-100% 15N], 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR3023C	[U-100% 13C; U-100% 15N]	0.51 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

4 3D CBCA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.51 mM [U-100% 13C; U-100% 15N], 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR3023C	[U-100% 13C; U-100% 15N]	0.51 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

5 3D HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.51 mM [U-100% 13C; U-100% 15N], 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR3023C	[U-100% 13C; U-100% 15N]	0.51 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

6 3D 1H-13C arom NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.51 mM [U-100% 13C; U-100% 15N], 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR3023C	[U-100% 13C; U-100% 15N]	0.51 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

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

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.51 mM [U-100% 13C; U-100% 15N], 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR3023C	[U-100% 13C; U-100% 15N]	0.51 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

8 2D 1H-13C HSQC aromatic

Instrument

Varian INOVA - 600 MHz at Rutgers

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.51 mM [U-100% 13C; U-100% 15N], 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR3023C	[U-100% 13C; U-100% 15N]	0.51 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

9 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz at University of Georgia

Sample

#	Name	Isotope labeling	Concentration
14	HR3023C	[U-100% 13C; U-100% 15N]	0.43 mM
15	NaN3	natural abundance	0.02 %
16	DTT	natural abundance	10 mM
17	CaCL2	natural abundance	5 mM
18	NaCL	natural abundance	100 mM
19	Proteinase Inhibitors	natural abundance	1 na
20	MES	natural abundance	20 mM
21	DSS	natural abundance	50 uM
22	D2O	natural abundance	10 %
23	H2O	natural abundance	90 %

10 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz at University of Georgia

Sample

#	Name	Isotope labeling	Concentration
24	HR3023C	[U-100% 13C; U-100% 15N]	0.43 mM
25	NaN3	natural abundance	0.02 %
26	DTT	natural abundance	10 mM
27	CaCL2	natural abundance	5 mM
28	NaCL	natural abundance	100 mM
29	Proteinase Inhibitors	natural abundance	1 na
30	MES	natural abundance	20 mM
31	DSS	natural abundance	50 uM
32	D2O	natural abundance	10 %
33	H2O	natural abundance	90 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_17683_2ldu.nef
Input source #2: Coordindates	2ldu.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
MGHHHHHHSHMAGPSNVPAFLTKLWTLVSDPDTDALICWSPSGNSFHVFDQGQFAKEVLPKYFKHNNMASFVRQLNMYGFRKVVHIEQGGLVKPERDDTE
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MGHHHHHHSHMAGPSNVPAFLTKLWTLVSDPDTDALICWSPSGNSFHVFDQGQFAKEVLPKYFKHNNMASFVRQLNMYGFRKVVHIEQGGLVKPERDDTE

-------110-------120-----
FQHPCFLRGQEQLLENIKRKVTSVS
|||||||||||||||||||||||||
FQHPCFLRGQEQLLENIKRKVTSVS

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	125	0	0	100.0

Content subtype: combined_17683_2ldu.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1360		92.0 (chain: A, length: 125)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	3404 (1)	noe	92.0 (chain: A, length: 125)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	38 (1)	hbond	26.4 (chain: A, length: 125)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	128 (128)	.	64.8 (chain: A, length: 125)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 125, Sequence coverage: 92.0%
- Total number of assignments
  - ¹H chemical shifts: 712
  - ¹³C chemical shifts: 528
  - ¹⁵N chemical shifts: 120
- 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)
15	SER	HG	4.838

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	781	711	91.0
¹³C chemical shifts	585	528	90.3
¹⁵N chemical shifts	138	120	87.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	251	227	90.4
¹³C chemical shifts	250	220	88.0
¹⁵N chemical shifts	118	105	89.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	530	484	91.3
¹³C chemical shifts	335	308	91.9
¹⁵N chemical shifts	20	15	75.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	60	59	98.3
¹³C chemical shifts	60	59	98.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	87	70	80.5
¹³C chemical shifts	85	68	80.0
¹⁵N chemical shifts	2	1	50.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 125, Sequence coverage: 92.0%
- Total number of restraints: 3398
- Weight of restraints: 1.0 (3398)
- Potential type of restraints: square-well-parabolic (3398)
- Range of distance target values: 2.22, 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_4
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 125, Sequence coverage: 26.4%
  - Total number of restraints: 38
  - Weight of restraints: 1.0 (38)
  - Potential type of restraints: square-well-parabolic (38)
  - Range of distance target values: 1.99, 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_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 125, Sequence coverage: 64.8%
- Total number of restraints: 128
- Total number of restraints per polymer type: 128
- Weight of restraints: 1.0 (128)
- Potential type of restraints: square-well-parabolic (128)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords DNA-binding, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG), Protein NMR, Protein Structure Initiative, Structural Genomics, Target HR3023C

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Found 1 Document (0.847 seconds)

BMRB: 17683

Sample #1

Sample #2

Sample #3

Sample #4

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. HR3023C, : 1 : 7 : 189 entities Detail

Interaction partners 1. HR3023C, : 3 interactors Detail

Experiments performed 10 experiments Detail

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NMR combined restraints 5 contents Detail