BMRBj - BMREntryMaster

Found 1 Document (0.683 seconds)

BMRB: 19299

2M9U

Analysis of target DNA binding sites through NMR structural analysis of the MLV IN CTD and homology modeling of the CCD domains.

Authors

Aiyer, S.S., Schneider, W.M., Chander, A., Roth, M.J., Montelione, G.T., Genomics Consortium, N., Rossi, P.

Assembly

MLV CTD IN

Entity

1. MLV CTD IN (polymer, Thiol state: not present), 91 monomers, 10296.65 Da Detail

MGHHHHHHSH MVGDTVWVRR HQTKNLEPRW KGPYTVLLTT PTALKVDGIA AWIHAAHVKA ADPGGGPSSR LTWRVQRSQN PLKIRLTREA P

Formula weight

10296.65 Da

Source organism

Murine leukemia virus

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 89.0 %, Completeness: 78.9 %, Completeness (bb): 86.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	78.9 % (836 of 1060)	75.7 % (417 of 551)	82.5 % (343 of 416)	81.7 % (76 of 93)
Backbone	86.8 % (462 of 532)	85.2 % (155 of 182)	88.3 % (235 of 266)	85.7 % (72 of 84)
Sidechain	73.4 % (449 of 612)	71.0 % (262 of 369)	78.2 % (183 of 234)	44.4 % (4 of 9)
Aromatic	60.4 % (58 of 96)	60.4 % (29 of 48)	56.8 % (25 of 44)	100.0 % (4 of 4)
Methyl	98.0 % (98 of 100)	98.0 % (49 of 50)	98.0 % (49 of 50)

1. OR41A-15.1

MGHHHHHHSH MVGDTVWVRR HQTKNLEPRW KGPYTVLLTT PTALKVDGIA AWIHAAHVKA ADPGGGPSSR LTWRVQRSQN PLKIRLTREA P

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.5mM OR41A-15.1, 10% D2O, 50 uM DSS, 100 mM NaCl, 50 mM potassium glutamate, 20 mM MES pH 6.5.

#	Name	Isotope labeling	Concentration
1	MLV IN CTD	[U-100% 13C; U-100% 15N]	0.5 mM
2	NaCl	natural abundance	100 mM
3	potassium glutamate	natural abundance	50 mM
4	MES	natural abundance	20 mM
5	DSS	natural abundance	50 uM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.5mM OR41A-15.1, 10% D2O, 50 uM DSS, 100 mM NaCl, 50 mM potassium glutamate, 20 mM MES pH 6.5.

#	Name	Isotope labeling	Concentration
6	MLV IN CTD	[U-10% 13C; U-100% 15N]	0.5 mM
7	NaCl	natural abundance	100 mM
8	potassium glutamate	natural abundance	50 mM
9	MES	natural abundance	20 mM
10	DSS	natural abundance	50 uM

LACS Plot; CA

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

Referencing offset: -0.06 ppm, Outliers: 3 Detail

LACS Plot; CB

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

Referencing offset: -0.06 ppm, Outliers: 3 Detail

LACS Plot; HA

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

Referencing offset: 0.04 ppm, Outliers: 1 Detail

LACS Plot; CO

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

Referencing offset: 0.36 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2M9U, Strand ID: A Detail

Release date

2013-12-15

Citation

Analysis of target DNA binding sites through NMR structural analysis of the MLV IN CTD and homology modeling of the CCD domains
Aiyer, S.S., Schneider, W.M., Chander, A., Montelione, G.T., Roth, M.J., Rossi, P.
Not known

Related entities 1. MLV CTD IN, : 1 : 1 : 24 entities Detail

Experiments performed 12 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 0.5mM OR41A-15.1, 10% D2O, 50 uM DSS, 100 mM NaCl, 50 mM potassium glutamate, 20 mM MES pH 6.5.

#	Name	Isotope labeling	Concentration
1	MLV IN CTD	[U-100% 13C; U-100% 15N]	0.5 mM
2	NaCl	natural abundance	100 mM
3	potassium glutamate	natural abundance	50 mM
4	MES	natural abundance	20 mM
5	DSS	natural abundance	50 uM

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	MLV IN CTD	[U-100% 13C; U-100% 15N]	0.5 mM
2	NaCl	natural abundance	100 mM
3	potassium glutamate	natural abundance	50 mM
4	MES	natural abundance	20 mM
5	DSS	natural abundance	50 uM

3 3D HNCO

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	MLV IN CTD	[U-100% 13C; U-100% 15N]	0.5 mM
2	NaCl	natural abundance	100 mM
3	potassium glutamate	natural abundance	50 mM
4	MES	natural abundance	20 mM
5	DSS	natural abundance	50 uM

4 3D CBCA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	MLV IN CTD	[U-100% 13C; U-100% 15N]	0.5 mM
2	NaCl	natural abundance	100 mM
3	potassium glutamate	natural abundance	50 mM
4	MES	natural abundance	20 mM
5	DSS	natural abundance	50 uM

5 3D HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	MLV IN CTD	[U-100% 13C; U-100% 15N]	0.5 mM
2	NaCl	natural abundance	100 mM
3	potassium glutamate	natural abundance	50 mM
4	MES	natural abundance	20 mM
5	DSS	natural abundance	50 uM

6 3D HBHA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	MLV IN CTD	[U-100% 13C; U-100% 15N]	0.5 mM
2	NaCl	natural abundance	100 mM
3	potassium glutamate	natural abundance	50 mM
4	MES	natural abundance	20 mM
5	DSS	natural abundance	50 uM

7 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	MLV IN CTD	[U-100% 13C; U-100% 15N]	0.5 mM
2	NaCl	natural abundance	100 mM
3	potassium glutamate	natural abundance	50 mM
4	MES	natural abundance	20 mM
5	DSS	natural abundance	50 uM

8 3D 13C-edited_NOESY

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	MLV IN CTD	[U-100% 13C; U-100% 15N]	0.5 mM
2	NaCl	natural abundance	100 mM
3	potassium glutamate	natural abundance	50 mM
4	MES	natural abundance	20 mM
5	DSS	natural abundance	50 uM

9 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	MLV IN CTD	[U-100% 13C; U-100% 15N]	0.5 mM
2	NaCl	natural abundance	100 mM
3	potassium glutamate	natural abundance	50 mM
4	MES	natural abundance	20 mM
5	DSS	natural abundance	50 uM

10 3D 13C-edited_NOESY

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	MLV IN CTD	[U-100% 13C; U-100% 15N]	0.5 mM
2	NaCl	natural abundance	100 mM
3	potassium glutamate	natural abundance	50 mM
4	MES	natural abundance	20 mM
5	DSS	natural abundance	50 uM

11 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
6	MLV IN CTD	[U-10% 13C; U-100% 15N]	0.5 mM
7	NaCl	natural abundance	100 mM
8	potassium glutamate	natural abundance	50 mM
9	MES	natural abundance	20 mM
10	DSS	natural abundance	50 uM

12 2D 1H-13C HSQC

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
6	MLV IN CTD	[U-10% 13C; U-100% 15N]	0.5 mM
7	NaCl	natural abundance	100 mM
8	potassium glutamate	natural abundance	50 mM
9	MES	natural abundance	20 mM
10	DSS	natural abundance	50 uM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19299_2m9u.nef
Input source #2: Coordindates	2m9u.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---------
HHHHHHSHMVGDTVWVRRHQTKNLEPRWKGPYTVLLTTPTALKVDGIAAWIHAAHVKAADPGGGPSSRLTWRVQRSQNPLKIRLTREAP
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
HHHHHHSHMVGDTVWVRRHQTKNLEPRWKGPYTVLLTTPTALKVDGIAAWIHAAHVKAADPGGGPSSRLTWRVQRSQNPLKIRLTREAP

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	89	0	0	100.0

Content subtype: combined_19299_2m9u.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	804		89.9 (chain: A, length: 89)
1	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	515 (1)	noe	74.2 (chain: A, length: 89)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	44 (1)	hbond	29.2 (chain: A, length: 89)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	147 (147)	.	70.8 (chain: A, length: 89)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 89, Sequence coverage: 89.9%
- Total number of assignments
  - ¹H chemical shifts: 396
  - ¹³C chemical shifts: 334
  - ¹⁵N chemical shifts: 74
- Completeness of assignments
  - Entity_assemble_ID: A
- Peptide bond of PRO
- 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	541	396	73.2
¹³C chemical shifts	409	334	81.7
¹⁵N chemical shifts	99	74	74.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	177	151	85.3
¹³C chemical shifts	178	158	88.8
¹⁵N chemical shifts	82	70	85.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	364	245	67.3
¹³C chemical shifts	231	176	76.2
¹⁵N chemical shifts	17	4	23.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	51	48	94.1
¹³C chemical shifts	51	50	98.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	48	28	58.3
¹³C chemical shifts	44	24	54.5
¹⁵N chemical shifts	4	4	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_4
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 89, Sequence coverage: 74.2%
- Total number of restraints: 513
- Weight of restraints: 1.0 (513)
- Potential type of restraints: square-well-parabolic (513)
- Range of distance target values: 2.59, 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_3
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 89, Sequence coverage: 29.2%
  - Total number of restraints: 44
  - Weight of restraints: 1.0 (44)
  - Potential type of restraints: square-well-parabolic (44)
  - Range of distance target values: 1.9, 2.85 (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: 89, Sequence coverage: 70.8%
- Total number of restraints: 147
- Total number of restraints per polymer type: 147
- Weight of restraints: 1.0 (147)
- Potential type of restraints: square-well-parabolic (147)
- Plot of Phi-Psi angle restraints
- Plot of Chi1-Chi2 angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Homology Modeling, MLV IN CTD/CCD, NESG, NMR solution structure, OR41A-15.1, PSI, SH3

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Found 1 Document (0.683 seconds)

BMRB: 19299

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. MLV CTD IN, : 1 : 1 : 24 entities Detail

Experiments performed 12 experiments Detail

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NMR combined restraints 5 contents Detail