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BMRB: 18589

2LVS

NMR solution structure of Cbp2

Authors

Kenchappa, C.S., Heidarsson, P.O., Garrett, R.A., Poulsen, F.M.

Assembly

Cbp2

Entity

1. Cbp2 (polymer, Thiol state: not present), 105 monomers, 12215.11 Da Detail

MPSVNDSLDI VEKLYKDGVP VKEIAKRSNN SMSTVYKALE KLEAMGRIKR RKGRYRQHRR LTEEELATIR ELYLKGATVY EIARQLGRPE STIYYALKKL GLKLE

Formula weight

12215.11 Da

Source organism

Hyperthermus butylicus

Exptl. method

Refine. method

DGSA-distance geometry simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 92.4 %, Completeness: 75.9 %, Completeness (bb): 89.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	75.9 % (975 of 1284)	70.9 % (483 of 681)	80.4 % (399 of 496)	86.9 % (93 of 107)
Backbone	89.4 % (558 of 624)	86.9 % (185 of 213)	90.6 % (280 of 309)	91.2 % (93 of 102)
Sidechain	66.5 % (505 of 759)	63.7 % (298 of 468)	72.4 % (207 of 286)	0.0 % (0 of 5)
Aromatic	33.3 % (20 of 60)	40.0 % (12 of 30)	26.7 % (8 of 30)
Methyl	86.3 % (107 of 124)	90.3 % (56 of 62)	82.3 % (51 of 62)

1. Cbp2

MPSVNDSLDI VEKLYKDGVP VKEIAKRSNN SMSTVYKALE KLEAMGRIKR RKGRYRQHRR LTEEELATIR ELYLKGATVY EIARQLGRPE STIYYALKKL GLKLE

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	Cbp2	[U-100% 13C; U-100% 15N]		0.5-1 mM
2	potassium chloride	none		10 mM
3	potassium dihydrogen phosphate	none		20 mM
4	sodium azide	none		0.02 %

LACS Plot; CA

Referencing offset: -0.23 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: -0.23 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: 0.07 ppm, Outliers: 3 Detail

LACS Plot; CO

Referencing offset: -0.45 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2013-01-15

Citation

Solution properties of the archaeal CRISPR DNA repeat-binding homeodomain protein Cbp2
Kenchappa, C.S., Heidarsson, P.O., Kragelund, B.B., Garrett, R.A., Poulsen, F.M.
Nucleic Acids Res. (2013), 41, 3424-3435, PubMed 23325851 , DOI 10.1093/nar/gks1465 , Abstract

Related entities 1. Cbp2, : 1 : 17 entities Detail

Experiments performed 10 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 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	Cbp2	[U-100% 13C; U-100% 15N]		0.5-1 mM
2	potassium chloride	none		10 mM
3	potassium dihydrogen phosphate	none		20 mM
4	sodium azide	none		0.02 %

2 3D CBCA(CO)NH

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	Cbp2	[U-100% 13C; U-100% 15N]		0.5-1 mM
2	potassium chloride	none		10 mM
3	potassium dihydrogen phosphate	none		20 mM
4	sodium azide	none		0.02 %

3 3D HNCO

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	Cbp2	[U-100% 13C; U-100% 15N]		0.5-1 mM
2	potassium chloride	none		10 mM
3	potassium dihydrogen phosphate	none		20 mM
4	sodium azide	none		0.02 %

4 3D HNCA

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	Cbp2	[U-100% 13C; U-100% 15N]		0.5-1 mM
2	potassium chloride	none		10 mM
3	potassium dihydrogen phosphate	none		20 mM
4	sodium azide	none		0.02 %

5 3D HNCACB

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	Cbp2	[U-100% 13C; U-100% 15N]		0.5-1 mM
2	potassium chloride	none		10 mM
3	potassium dihydrogen phosphate	none		20 mM
4	sodium azide	none		0.02 %

6 3D HN(CO)CA

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	Cbp2	[U-100% 13C; U-100% 15N]		0.5-1 mM
2	potassium chloride	none		10 mM
3	potassium dihydrogen phosphate	none		20 mM
4	sodium azide	none		0.02 %

7 3D HCCH-TOCSY

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	Cbp2	[U-100% 13C; U-100% 15N]		0.5-1 mM
2	potassium chloride	none		10 mM
3	potassium dihydrogen phosphate	none		20 mM
4	sodium azide	none		0.02 %

8 3D 1H-15N NOESY

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	Cbp2	[U-100% 13C; U-100% 15N]		0.5-1 mM
2	potassium chloride	none		10 mM
3	potassium dihydrogen phosphate	none		20 mM
4	sodium azide	none		0.02 %

9 3D 1H-13C NOESY

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	Cbp2	[U-100% 13C; U-100% 15N]		0.5-1 mM
2	potassium chloride	none		10 mM
3	potassium dihydrogen phosphate	none		20 mM
4	sodium azide	none		0.02 %

10 3D HN(COCA)CB

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	Cbp2	[U-100% 13C; U-100% 15N]		0.5-1 mM
2	potassium chloride	none		10 mM
3	potassium dihydrogen phosphate	none		20 mM
4	sodium azide	none		0.02 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18589_2lvs.nef
Input source #2: Coordindates	2lvs.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
MPSVNDSLDIVEKLYKDGVPVKEIAKRSNNSMSTVYKALEKLEAMGRIKRRKGRYRQHRRLTEEELATIRELYLKGATVYEIARQLGRPESTIYYALKKL
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MPSVNDSLDIVEKLYKDGVPVKEIAKRSNNSMSTVYKALEKLEAMGRIKRRKGRYRQHRRLTEEELATIRELYLKGATVYEIARQLGRPESTIYYALKKL

-----
GLKLE
|||||
GLKLE

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	105	0	0	100.0

Content subtype: combined_18589_2lvs.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1009		89.5 (chain: A, length: 105)
1	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	1767 (1)	noe	86.7 (chain: A, length: 105)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_2	OK	157 (157)	.	85.7 (chain: A, length: 105)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 105, Sequence coverage: 89.5%
- Total number of assignments
  - ¹H chemical shifts: 525
  - ¹³C chemical shifts: 395
  - ¹⁵N chemical shifts: 89
- 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

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_3
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 105, Sequence coverage: 86.7%
- Total number of restraints: 1767
- Weight of restraints: 1.0 (1767)
- Potential type of restraints: upper-bound-parabolic (1767)
- Range of distance target values: 2.33, 5.5 (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: DYANA/DIANA_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 105, Sequence coverage: 85.7%
- Total number of restraints: 157
- Total number of restraints per polymer type: 157
- Weight of restraints: 1.0 (157)
- Potential type of restraints: square-well-parabolic (157)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Protein