BMRBj - BMREntryMaster

Found 1 Document (0.708 seconds)

BMRB: 18714

2LY9

Solution NMR Structure of Homeobox 2 Domain from Human ZHX1 repressor, Northeast Structural Genomics Consortium (NESG) Target HR7907F

Authors

Xu, X., Eletsky, A., Mills, J.L., Pulavarti, S.VSRK., Lee, D., Kohan, E., Janjua, H., Xiao, R., Acton, T.B., Everett, J.K., Montelione, G.T., Szyperski, T.

Assembly

HR7907F

Entity

1. HR7907F (polymer, Thiol state: all free), 74 monomers, 8692.877 Da Detail

SHMPDSFGIR AKKTKEQLAE LKVSYLKNQF PHDSEIIRLM KITGLTKGEI KKWFSDTRYN QRNSKSNQCL HLNN

Formula weight

8692.877 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.3 %, Completeness: 94.8 %, Completeness (bb): 94.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	94.8 % (875 of 923)	94.7 % (465 of 491)	94.8 % (331 of 349)	95.2 % (79 of 83)
Backbone	94.3 % (415 of 440)	94.6 % (141 of 149)	94.1 % (206 of 219)	94.4 % (68 of 72)
Sidechain	95.3 % (528 of 554)	94.7 % (324 of 342)	96.0 % (193 of 201)	100.0 % (11 of 11)
Aromatic	85.7 % (60 of 70)	80.0 % (28 of 35)	91.2 % (31 of 34)	100.0 % (1 of 1)
Methyl	100.0 % (64 of 64)	100.0 % (32 of 32)	100.0 % (32 of 32)

1. HR7907F

SHMPDSFGIR AKKTKEQLAE LKVSYLKNQF PHDSEIIRLM KITGLTKGEI KKWFSDTRYN QRNSKSNQCL HLNN

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 0.4 mM HR7907F, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR7907F	[U-100% 13C; U-100% 15N]	0.4 mM
2	sodium azide	natural abundance	0.02 %
3	DTT	natural abundance	10 mM
4	calcium chloride	natural abundance	5 mM
5	sodium chloride	natural abundance	100 mM
6	Proteinase Inhibitors	natural abundance	1 na
7	MES	natural abundance	20 mM
8	DSS	natural abundance	50 uM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 0.3 mM HR7907F, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
11	HR7907F	[5% 13C; U-100% 15N]	0.3 mM
12	sodium azide	natural abundance	0.02 %
13	DTT	natural abundance	10 mM
14	calcium chloride	natural abundance	5 mM
15	sodium chloride	natural abundance	100 mM
16	Proteinase Inhibitors	natural abundance	1 na
17	MES	natural abundance	20 mM
18	DSS	natural abundance	50 uM
19	H2O	natural abundance	90 %
20	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: 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: -0.06 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	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: 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: -0.28 ppm, Outliers: 3 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2LY9, Strand ID: A Detail

Release date

2012-11-11

Related entities 1. HR7907F, : 1 : 9 : 89 entities Detail

Interaction partners 1. HR7907F, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 0.4 mM HR7907F, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR7907F	[U-100% 13C; U-100% 15N]	0.4 mM
2	sodium azide	natural abundance	0.02 %
3	DTT	natural abundance	10 mM
4	calcium chloride	natural abundance	5 mM
5	sodium chloride	natural abundance	100 mM
6	Proteinase Inhibitors	natural abundance	1 na
7	MES	natural abundance	20 mM
8	DSS	natural abundance	50 uM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

2 2D 1H-13C HSQC

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 0.4 mM HR7907F, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR7907F	[U-100% 13C; U-100% 15N]	0.4 mM
2	sodium azide	natural abundance	0.02 %
3	DTT	natural abundance	10 mM
4	calcium chloride	natural abundance	5 mM
5	sodium chloride	natural abundance	100 mM
6	Proteinase Inhibitors	natural abundance	1 na
7	MES	natural abundance	20 mM
8	DSS	natural abundance	50 uM
9	H2O	natural abundance	90 %
10	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 273 K, pH 6.5, Details 0.4 mM HR7907F, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR7907F	[U-100% 13C; U-100% 15N]	0.4 mM
2	sodium azide	natural abundance	0.02 %
3	DTT	natural abundance	10 mM
4	calcium chloride	natural abundance	5 mM
5	sodium chloride	natural abundance	100 mM
6	Proteinase Inhibitors	natural abundance	1 na
7	MES	natural abundance	20 mM
8	DSS	natural abundance	50 uM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

4 (4,3)D GFT CABCA(CO)NHN

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 0.4 mM HR7907F, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR7907F	[U-100% 13C; U-100% 15N]	0.4 mM
2	sodium azide	natural abundance	0.02 %
3	DTT	natural abundance	10 mM
4	calcium chloride	natural abundance	5 mM
5	sodium chloride	natural abundance	100 mM
6	Proteinase Inhibitors	natural abundance	1 na
7	MES	natural abundance	20 mM
8	DSS	natural abundance	50 uM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

5 (4,3)D GFT HNNCABCA

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 0.4 mM HR7907F, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR7907F	[U-100% 13C; U-100% 15N]	0.4 mM
2	sodium azide	natural abundance	0.02 %
3	DTT	natural abundance	10 mM
4	calcium chloride	natural abundance	5 mM
5	sodium chloride	natural abundance	100 mM
6	Proteinase Inhibitors	natural abundance	1 na
7	MES	natural abundance	20 mM
8	DSS	natural abundance	50 uM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

6 2D 1H-13C HSQC

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 0.3 mM HR7907F, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
11	HR7907F	[5% 13C; U-100% 15N]	0.3 mM
12	sodium azide	natural abundance	0.02 %
13	DTT	natural abundance	10 mM
14	calcium chloride	natural abundance	5 mM
15	sodium chloride	natural abundance	100 mM
16	Proteinase Inhibitors	natural abundance	1 na
17	MES	natural abundance	20 mM
18	DSS	natural abundance	50 uM
19	H2O	natural abundance	90 %
20	D2O	natural abundance	10 %

7 (4,3)D GFT HCCH-COSY alipahtic

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 0.4 mM HR7907F, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR7907F	[U-100% 13C; U-100% 15N]	0.4 mM
2	sodium azide	natural abundance	0.02 %
3	DTT	natural abundance	10 mM
4	calcium chloride	natural abundance	5 mM
5	sodium chloride	natural abundance	100 mM
6	Proteinase Inhibitors	natural abundance	1 na
7	MES	natural abundance	20 mM
8	DSS	natural abundance	50 uM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

8 3D (H)CCH-TOCSY aliphatic

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 0.4 mM HR7907F, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR7907F	[U-100% 13C; U-100% 15N]	0.4 mM
2	sodium azide	natural abundance	0.02 %
3	DTT	natural abundance	10 mM
4	calcium chloride	natural abundance	5 mM
5	sodium chloride	natural abundance	100 mM
6	Proteinase Inhibitors	natural abundance	1 na
7	MES	natural abundance	20 mM
8	DSS	natural abundance	50 uM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

9 3D 13C/15N-edited NOESY

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 0.4 mM HR7907F, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR7907F	[U-100% 13C; U-100% 15N]	0.4 mM
2	sodium azide	natural abundance	0.02 %
3	DTT	natural abundance	10 mM
4	calcium chloride	natural abundance	5 mM
5	sodium chloride	natural abundance	100 mM
6	Proteinase Inhibitors	natural abundance	1 na
7	MES	natural abundance	20 mM
8	DSS	natural abundance	50 uM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

10 (4,3)D GFT HABCAB(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 0.4 mM HR7907F, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR7907F	[U-100% 13C; U-100% 15N]	0.4 mM
2	sodium azide	natural abundance	0.02 %
3	DTT	natural abundance	10 mM
4	calcium chloride	natural abundance	5 mM
5	sodium chloride	natural abundance	100 mM
6	Proteinase Inhibitors	natural abundance	1 na
7	MES	natural abundance	20 mM
8	DSS	natural abundance	50 uM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

11 3D (H)CCH-COSY aromatic

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 0.4 mM HR7907F, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR7907F	[U-100% 13C; U-100% 15N]	0.4 mM
2	sodium azide	natural abundance	0.02 %
3	DTT	natural abundance	10 mM
4	calcium chloride	natural abundance	5 mM
5	sodium chloride	natural abundance	100 mM
6	Proteinase Inhibitors	natural abundance	1 na
7	MES	natural abundance	20 mM
8	DSS	natural abundance	50 uM
9	H2O	natural abundance	90 %
10	D2O	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_18714_2ly9.nef
Input source #2: Coordindates	2ly9.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----
SHMPDSFGIRAKKTKEQLAELKVSYLKNQFPHDSEIIRLMKITGLTKGEIKKWFSDTRYNQRNSKSNQCLHLNN
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
SHMPDSFGIRAKKTKEQLAELKVSYLKNQFPHDSEIIRLMKITGLTKGEIKKWFSDTRYNQRNSKSNQCLHLNN

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	74	0	0	100.0

Content subtype: combined_18714_2ly9.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	886		95.9 (chain: A, length: 74)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	1190 (1)	noe	89.2 (chain: A, length: 74)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	62 (62)	.	50.0 (chain: A, length: 74)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 74, Sequence coverage: 95.9%
- Total number of assignments
  - ¹H chemical shifts: 471
  - ¹³C chemical shifts: 332
  - ¹⁵N chemical shifts: 83
- 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)
32	HIS	ND1	232.758
32	HIS	NE2	171.036
57	THR	HG1	2.13
71	HIS	ND1	202.568
71	HIS	NE2	176.749

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	491	470	95.7
¹³C chemical shifts	349	332	95.1
¹⁵N chemical shifts	87	79	90.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	149	142	95.3
¹³C chemical shifts	148	139	93.9
¹⁵N chemical shifts	72	67	93.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	342	328	95.9
¹³C chemical shifts	201	193	96.0
¹⁵N chemical shifts	15	12	80.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	34	33	97.1
¹³C chemical shifts	34	33	97.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	35	32	91.4
¹³C chemical shifts	34	31	91.2
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: 74, Sequence coverage: 89.2%
- Total number of restraints: 1186
- Weight of restraints: 1.0 (1186)
- Potential type of restraints: square-well-parabolic (1186)
- Range of distance target values: 1.3, 3.02 (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

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 74, Sequence coverage: 50.0%
- Total number of restraints: 62
- Total number of restraints per polymer type: 62
- Weight of restraints: 1.0 (62)
- Potential type of restraints: square-well-parabolic (62)
- 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 HR7907F

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Found 1 Document (0.708 seconds)

BMRB: 18714

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. HR7907F, : 1 : 9 : 89 entities Detail

Interaction partners 1. HR7907F, : 1 interactors Detail

Experiments performed 11 experiments Detail

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NMR combined restraints 4 contents Detail