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Found 1 Document (1.078 seconds)

BMRB: 16636

2KRF

NMR solution structure of the DNA binding domain of Competence protein A

Authors

Hobbs, C.A., Bobay, B.G., Thompson, R.J., Perego, M., Cavanagh, J.

Assembly

ComAC

Entity

1. ComAC (polymer, Thiol state: all free), 73 monomers, 8075.059 × 2 Da Detail

GSHMSSQKEQ DVLTPRECLI LQEVEKGFTN QEIADALHLS KRSIEYSLTS IFNKLNVGSR TEAVLIAKSD GVL

Total weight

16150.118 Da

Max. entity weight

8075.059 Da

Source organism

Bacillus subtilis

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.6 %, Completeness: 84.3 %, Completeness (bb): 95.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	84.3 % (708 of 840)	78.4 % (342 of 436)	90.5 % (294 of 325)	91.1 % (72 of 79)
Backbone	95.6 % (417 of 436)	95.3 % (142 of 149)	95.3 % (205 of 215)	97.2 % (70 of 72)
Sidechain	75.7 % (358 of 473)	69.7 % (200 of 287)	87.2 % (156 of 179)	28.6 % (2 of 7)
Aromatic	0.0 % (0 of 36)	0.0 % (0 of 18)	0.0 % (0 of 18)
Methyl	94.6 % (87 of 92)	91.3 % (42 of 46)	97.8 % (45 of 46)

1. ComAC

GSHMSSQKEQ DVLTPRECLI LQEVEKGFTN QEIADALHLS KRSIEYSLTS IFNKLNVGSR TEAVLIAKSD GVL

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Temperature 288 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	25 mM
2	sodium chloride	natural abundance	100 mM
3	DTT	natural abundance	1 mM
4	EDTA	natural abundance	2 mM
5	ComAC	[U-13C; U-15N]	1 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

Sample #2

Solvent system 100% D2O, Temperature 288 K, pH 6.5

#	Name	Isotope labeling	Concentration
8	sodium phosphate	natural abundance	25 mM
9	sodium chloride	natural abundance	100 mM
10	DTT	natural abundance	1 mM
11	EDTA	natural abundance	2 mM
12	ComAC	[U-13C; U-15N]	1 mM
13	D2O	natural abundance	100 %

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: -0.79 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: -0.79 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: -0.32 ppm, Outliers: 2 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: -0.99 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 2KRF, Strand ID: A, B Detail

Release date

2009-12-16

Citation

NMR solution structure and DNA-binding model of the DNA-binding domain of competence protein A
Hobbs, C.A., Bobay, B.G., Thompson, R.J., Perego, M., Cavanagh, J.
J. Mol. Biol. (2010), 398, 248-263, PubMed 20302877 , DOI 10.1016/j.jmb.2010.03.003 , Abstract

Related entities 1. ComAC, : 1 : 1 : 1 : 78 entities Detail

Interaction partners 1. ComAC, : 2 interactors Detail

More details for 2 interactors identified by 2 citations

Experiments performed 12 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 288 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	25 mM
2	sodium chloride	natural abundance	100 mM
3	DTT	natural abundance	1 mM
4	EDTA	natural abundance	2 mM
5	ComAC	[U-13C; U-15N]	1 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

2 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 288 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	25 mM
2	sodium chloride	natural abundance	100 mM
3	DTT	natural abundance	1 mM
4	EDTA	natural abundance	2 mM
5	ComAC	[U-13C; U-15N]	1 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

3 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 288 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	25 mM
2	sodium chloride	natural abundance	100 mM
3	DTT	natural abundance	1 mM
4	EDTA	natural abundance	2 mM
5	ComAC	[U-13C; U-15N]	1 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

4 3D C(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 288 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	25 mM
2	sodium chloride	natural abundance	100 mM
3	DTT	natural abundance	1 mM
4	EDTA	natural abundance	2 mM
5	ComAC	[U-13C; U-15N]	1 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

5 3D HNCO

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 288 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	25 mM
2	sodium chloride	natural abundance	100 mM
3	DTT	natural abundance	1 mM
4	EDTA	natural abundance	2 mM
5	ComAC	[U-13C; U-15N]	1 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

6 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 288 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	25 mM
2	sodium chloride	natural abundance	100 mM
3	DTT	natural abundance	1 mM
4	EDTA	natural abundance	2 mM
5	ComAC	[U-13C; U-15N]	1 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

7 3D HN(CO)CA

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 288 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	25 mM
2	sodium chloride	natural abundance	100 mM
3	DTT	natural abundance	1 mM
4	EDTA	natural abundance	2 mM
5	ComAC	[U-13C; U-15N]	1 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

8 3D H(CCO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 288 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	25 mM
2	sodium chloride	natural abundance	100 mM
3	DTT	natural abundance	1 mM
4	EDTA	natural abundance	2 mM
5	ComAC	[U-13C; U-15N]	1 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

9 3D HCCH-TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Temperature 288 K, pH 6.5

#	Name	Isotope labeling	Concentration
8	sodium phosphate	natural abundance	25 mM
9	sodium chloride	natural abundance	100 mM
10	DTT	natural abundance	1 mM
11	EDTA	natural abundance	2 mM
12	ComAC	[U-13C; U-15N]	1 mM
13	D2O	natural abundance	100 %

10 3D 1H-15N NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 288 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	25 mM
2	sodium chloride	natural abundance	100 mM
3	DTT	natural abundance	1 mM
4	EDTA	natural abundance	2 mM
5	ComAC	[U-13C; U-15N]	1 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

11 3D 1H-13C NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 288 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	25 mM
2	sodium chloride	natural abundance	100 mM
3	DTT	natural abundance	1 mM
4	EDTA	natural abundance	2 mM
5	ComAC	[U-13C; U-15N]	1 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

12 3D 1H-15N TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 288 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	25 mM
2	sodium chloride	natural abundance	100 mM
3	DTT	natural abundance	1 mM
4	EDTA	natural abundance	2 mM
5	ComAC	[U-13C; U-15N]	1 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_16636_2krf.nef
Input source #2: Coordindates	2krf.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

------150-------160-------170-------180-------190-------200-------210----
GSHMSSQKEQDVLTPRECLILQEVEKGFTNQEIADALHLSKRSIEYSLTSIFNKLNVGSRTEAVLIAKSDGVL
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSHMSSQKEQDVLTPRECLILQEVEKGFTNQEIADALHLSKRSIEYSLTSIFNKLNVGSRTEAVLIAKSDGVL
--------10--------20--------30--------40--------50--------60--------70---

Entity_assembly_ID (NMR): B vs Auth_asym_ID (model): B

------150-------160-------170-------180-------190-------200-------210----
GSHMSSQKEQDVLTPRECLILQEVEKGFTNQEIADALHLSKRSIEYSLTSIFNKLNVGSRTEAVLIAKSDGVL
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSHMSSQKEQDVLTPRECLILQEVEKGFTNQEIADALHLSKRSIEYSLTSIFNKLNVGSRTEAVLIAKSDGVL
--------10--------20--------30--------40--------50--------60--------70---

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	73	0	0	100.0
B	B	73	0	0	100.0

Content subtype: combined_16636_2krf.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	688		98.6 (chain: A, length: 73)
1	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	14374 (1)	noe	97.3 (chain: A, length: 73), 97.3 (chain: B, length: 73)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	102 (1)	hbond	56.2 (chain: A, length: 73), 56.2 (chain: B, length: 73)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 73, Sequence coverage: 98.6%
- Total number of assignments
  - ¹H chemical shifts: 327
  - ¹³C chemical shifts: 292
  - ¹⁵N chemical shifts: 69
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
170	THR	HG1	1.775

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	436	316	72.5
¹³C chemical shifts	325	292	89.8
¹⁵N chemical shifts	82	69	84.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	149	143	96.0
¹³C chemical shifts	146	139	95.2
¹⁵N chemical shifts	72	69	95.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	287	173	60.3
¹³C chemical shifts	179	153	85.5
¹⁵N chemical shifts	10	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	47	40	85.1
¹³C chemical shifts	47	42	89.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	18	0	0.0
¹³C chemical shifts	18	0	0.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_4
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 73, Sequence coverage: 97.3%
  - Entity_assembly_ID: B, Chain length: 73, Sequence coverage: 97.3%
- Total number of restraints: 14364
- Weight of restraints: 1.0 (14364)
- Potential type of restraints: square-well-parabolic (14364)
- Range of distance target values: 1.7, 4.0 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 73, Sequence coverage: 56.2%
    - Entity_assembly_ID: B, Chain length: 73, Sequence coverage: 56.2%
  - Total number of restraints: 102
  - Weight of restraints: 1.0 (102)
  - Potential type of restraints: square-well-parabolic (102)
  - Range of distance target values: 1.95, 2.9 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
  - Distance restraints on contact map

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Found 1 Document (1.078 seconds)

BMRB: 16636

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. ComAC, : 1 : 1 : 1 : 78 entities Detail

Interaction partners 1. ComAC, : 2 interactors Detail

Experiments performed 12 experiments Detail

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NMR combined restraints 4 contents Detail