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Found 1 Document (0.666 seconds)

BMRB: 15314

2JR1

Solution structure of the DNA binding domain of a nucleoid-associated protein, H-NS, from the phytopathogen Xylella fastidiosa.

Authors

Rosselli, L.K., Sforca, M.L., Souza, A.P., Zeri, A.C.

Assembly

HNS79c monomer

Entity

1. HNS79c monomer (polymer, Thiol state: not present), 79 monomers, 8830.109 Da Detail

FNVKQKSEIT ALVKEVTPPR KAPSKAKREA PIKYWLPHSG ATWSGRGKIP KPFEAWIGTA AYTAWKAKHP DEKFPAFPG

Formula weight

8830.109 Da

Source organism

Xylella fastidiosa

Exptl. method

solution NMR

Refine. method

torsion angle dynamics, minimization

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.7 %, Completeness: 86.2 %, Completeness (bb): 95.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	86.2 % (833 of 966)	89.2 % (455 of 510)	79.8 % (304 of 381)	98.7 % (74 of 75)
Backbone	95.8 % (435 of 454)	98.7 % (151 of 153)	93.1 % (216 of 232)	98.6 % (68 of 69)
Sidechain	80.4 % (471 of 586)	85.2 % (304 of 357)	72.2 % (161 of 223)	100.0 % (6 of 6)
Aromatic	59.8 % (67 of 112)	60.7 % (34 of 56)	55.8 % (29 of 52)	100.0 % (4 of 4)
Methyl	83.8 % (57 of 68)	91.2 % (31 of 34)	76.5 % (26 of 34)

1. protein HNS79c

FNVKQKSEIT ALVKEVTPPR KAPSKAKREA PIKYWLPHSG ATWSGRGKIP KPFEAWIGTA AYTAWKAKHP DEKFPAFPG

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 (±0.2) K, pH 6.8 (±0.5)

#	Name	Isotope labeling	Concentration
1	protein_HNS79c	[U-99% 13C; U-99% 15N]	0.5 mM
2	sodium phosphate	natural abundance	50 mM
3	NaCl	natural abundance	200 mM
4	sodium azide	natural abundance	1 %
5	H2O	natural abundance	95 %
6	D2O		5 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 293 (±0.2) K, pH 6.8 (±0.5)

#	Name	Isotope labeling	Concentration
7	protein_HNS79c	[U-99% 13C; U-99% 15N]	0.5 mM
8	sodium phosphate	natural abundance	50 mM
9	NaCl	natural abundance	200 mM
10	sodium azide	natural abundance	1 %
11	D2O		100 %

Sample #3

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 (±0.2) K, pH 6.8 (±0.5)

#	Name	Isotope labeling	Concentration
12	protein_HNS79c	[U-99% 15N]	0.5 mM
13	sodium phosphate	natural abundance	50 mM
14	NaCl	natural abundance	200 mM
15	sodium azide	natural abundance	1 %
16	H2O	natural abundance	95 %
17	D2O		5 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	ubiquitin	methyl carbon	56.0 ppm	external	direct	1.0
¹H	water	protons	4.8 ppm	internal	direct	1.0
¹⁵N	ubiquitin	nitrogen	119.0 ppm	external	direct	1.0

Referencing offset: 0.89 ppm, Outliers: 2 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	ubiquitin	methyl carbon	56.0 ppm	external	direct	1.0
¹H	water	protons	4.8 ppm	internal	direct	1.0
¹⁵N	ubiquitin	nitrogen	119.0 ppm	external	direct	1.0

Referencing offset: 0.89 ppm, Outliers: 2 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	ubiquitin	methyl carbon	56.0 ppm	external	direct	1.0
¹H	water	protons	4.8 ppm	internal	direct	1.0
¹⁵N	ubiquitin	nitrogen	119.0 ppm	external	direct	1.0

Referencing offset: -0.01 ppm, Outliers: 3 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	ubiquitin	methyl carbon	56.0 ppm	external	direct	1.0
¹H	water	protons	4.8 ppm	internal	direct	1.0
¹⁵N	ubiquitin	nitrogen	119.0 ppm	external	direct	1.0

Referencing offset: -1.59 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2JR1, Strand ID: A Detail

Release date

2009-10-13

Citation

Solution structure of the DNA binding domain of a nucleoid-associated protein, H-NS, from the phytopathogen Xylella fastidiosa
Rosselli, L.K., Sforca, M.L., Souza, A.P., Zeri, A.C.
Not known

Related entities 1. HNS79c monomer, : 1 : 5 entities Detail

Experiments performed 14 experiments Detail

1 3D HNCACB

Instrument

Varian INOVA - 600 MHz HNC Triple resonance probe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 (±0.2) K, pH 6.8 (±0.5)

#	Name	Isotope labeling	Concentration
1	protein_HNS79c	[U-99% 13C; U-99% 15N]	0.5 mM
2	sodium phosphate	natural abundance	50 mM
3	NaCl	natural abundance	200 mM
4	sodium azide	natural abundance	1 %
5	H2O	natural abundance	95 %
6	D2O		5 %

2 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz HNC Triple resonance probe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 (±0.2) K, pH 6.8 (±0.5)

#	Name	Isotope labeling	Concentration
1	protein_HNS79c	[U-99% 13C; U-99% 15N]	0.5 mM
2	sodium phosphate	natural abundance	50 mM
3	NaCl	natural abundance	200 mM
4	sodium azide	natural abundance	1 %
5	H2O	natural abundance	95 %
6	D2O		5 %

3 3D HCCH-TOCSY

Instrument

Varian INOVA - 600 MHz HNC Triple resonance probe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 (±0.2) K, pH 6.8 (±0.5)

#	Name	Isotope labeling	Concentration
7	protein_HNS79c	[U-99% 13C; U-99% 15N]	0.5 mM
8	sodium phosphate	natural abundance	50 mM
9	NaCl	natural abundance	200 mM
10	sodium azide	natural abundance	1 %
11	D2O		100 %

4 3D CCH-TOCSY

Instrument

Varian INOVA - 600 MHz HNC Triple resonance probe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 (±0.2) K, pH 6.8 (±0.5)

#	Name	Isotope labeling	Concentration
7	protein_HNS79c	[U-99% 13C; U-99% 15N]	0.5 mM
8	sodium phosphate	natural abundance	50 mM
9	NaCl	natural abundance	200 mM
10	sodium azide	natural abundance	1 %
11	D2O		100 %

5 3D 1H-15N TOCSY

Instrument

Varian INOVA - 600 MHz HNC Triple resonance probe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 (±0.2) K, pH 6.8 (±0.5)

#	Name	Isotope labeling	Concentration
1	protein_HNS79c	[U-99% 13C; U-99% 15N]	0.5 mM
2	sodium phosphate	natural abundance	50 mM
3	NaCl	natural abundance	200 mM
4	sodium azide	natural abundance	1 %
5	H2O	natural abundance	95 %
6	D2O		5 %

6 3D 1H-15N NOESY

Instrument

Varian INOVA - 600 MHz HNC Triple resonance probe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 (±0.2) K, pH 6.8 (±0.5)

#	Name	Isotope labeling	Concentration
1	protein_HNS79c	[U-99% 13C; U-99% 15N]	0.5 mM
2	sodium phosphate	natural abundance	50 mM
3	NaCl	natural abundance	200 mM
4	sodium azide	natural abundance	1 %
5	H2O	natural abundance	95 %
6	D2O		5 %

7 3D 1H-15N NOESY

Instrument

Varian INOVA - 500 MHz HNC Triple resonance probe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 (±0.2) K, pH 6.8 (±0.5)

#	Name	Isotope labeling	Concentration
1	protein_HNS79c	[U-99% 13C; U-99% 15N]	0.5 mM
2	sodium phosphate	natural abundance	50 mM
3	NaCl	natural abundance	200 mM
4	sodium azide	natural abundance	1 %
5	H2O	natural abundance	95 %
6	D2O		5 %

8 3D 1H-13C NOESY

Instrument

Varian INOVA - 600 MHz HNC Triple resonance probe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 (±0.2) K, pH 6.8 (±0.5)

#	Name	Isotope labeling	Concentration
7	protein_HNS79c	[U-99% 13C; U-99% 15N]	0.5 mM
8	sodium phosphate	natural abundance	50 mM
9	NaCl	natural abundance	200 mM
10	sodium azide	natural abundance	1 %
11	D2O		100 %

9 Heteronuclear NOE

Instrument

Varian INOVA - 500 MHz HNC Triple resonance probe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 (±0.2) K, pH 6.8 (±0.5)

#	Name	Isotope labeling	Concentration
12	protein_HNS79c	[U-99% 15N]	0.5 mM
13	sodium phosphate	natural abundance	50 mM
14	NaCl	natural abundance	200 mM
15	sodium azide	natural abundance	1 %
16	H2O	natural abundance	95 %
17	D2O		5 %

10 Heteronuclear NOE

Instrument

Varian INOVA - 600 MHz HNC Triple resonance probe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 (±0.2) K, pH 6.8 (±0.5)

#	Name	Isotope labeling	Concentration
12	protein_HNS79c	[U-99% 15N]	0.5 mM
13	sodium phosphate	natural abundance	50 mM
14	NaCl	natural abundance	200 mM
15	sodium azide	natural abundance	1 %
16	H2O	natural abundance	95 %
17	D2O		5 %

11 T1 Relaxation

Instrument

Varian INOVA - 500 MHz HNC Triple resonance probe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 (±0.2) K, pH 6.8 (±0.5)

#	Name	Isotope labeling	Concentration
12	protein_HNS79c	[U-99% 15N]	0.5 mM
13	sodium phosphate	natural abundance	50 mM
14	NaCl	natural abundance	200 mM
15	sodium azide	natural abundance	1 %
16	H2O	natural abundance	95 %
17	D2O		5 %

12 T1 Relaxation

Instrument

Varian INOVA - 600 MHz HNC Triple resonance probe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 (±0.2) K, pH 6.8 (±0.5)

#	Name	Isotope labeling	Concentration
12	protein_HNS79c	[U-99% 15N]	0.5 mM
13	sodium phosphate	natural abundance	50 mM
14	NaCl	natural abundance	200 mM
15	sodium azide	natural abundance	1 %
16	H2O	natural abundance	95 %
17	D2O		5 %

13 T2 Relaxation

Instrument

Varian INOVA - 500 MHz HNC Triple resonance probe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 (±0.2) K, pH 6.8 (±0.5)

#	Name	Isotope labeling	Concentration
12	protein_HNS79c	[U-99% 15N]	0.5 mM
13	sodium phosphate	natural abundance	50 mM
14	NaCl	natural abundance	200 mM
15	sodium azide	natural abundance	1 %
16	H2O	natural abundance	95 %
17	D2O		5 %

14 T2 Relaxation

Instrument

Varian INOVA - 600 MHz HNC Triple resonance probe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 (±0.2) K, pH 6.8 (±0.5)

#	Name	Isotope labeling	Concentration
12	protein_HNS79c	[U-99% 15N]	0.5 mM
13	sodium phosphate	natural abundance	50 mM
14	NaCl	natural abundance	200 mM
15	sodium azide	natural abundance	1 %
16	H2O	natural abundance	95 %
17	D2O		5 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_15314_2jr1.nef
Input source #2: Coordindates	2jr1.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---------
FNVKQKSEITALVKEVTPPRKAPSKAKREAPIKYWLPHSGATWSGRGKIPKPFEAWIGTAAYTAWKAKHPDEKFPAFPG
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
FNVKQKSEITALVKEVTPPRKAPSKAKREAPIKYWLPHSGATWSGRGKIPKPFEAWIGTAAYTAWKAKHPDEKFPAFPG

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	79	0	0	100.0

Content subtype: combined_15314_2jr1.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assignments_HNS79c	Warning	831		98.7 (chain: A, length: 79)
1	Distance restraints	Discover_distance_constraints_2	Warning	1345 (1)	noe	100.0 (chain: A, length: 79)

Assigned chemical shifts

Saveframe: assignments_HNS79c
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 79, Sequence coverage: 98.7%
- Total number of assignments
  - ¹H chemical shifts: 454
  - ¹³C chemical shifts: 303
  - ¹⁵N chemical shifts: 74
- Completeness of assignments
  - Entity_assemble_ID: A
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	510	454	89.0
¹³C chemical shifts	381	303	79.5
¹⁵N chemical shifts	78	74	94.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	153	151	98.7
¹³C chemical shifts	158	142	89.9
¹⁵N chemical shifts	69	68	98.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	357	303	84.9
¹³C chemical shifts	223	161	72.2
¹⁵N chemical shifts	9	6	66.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	34	31	91.2
¹³C chemical shifts	34	26	76.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	56	34	60.7
¹³C chemical shifts	52	29	55.8
¹⁵N chemical shifts	4	4	100.0

Distance restraints

Saveframe: Discover_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 79, Sequence coverage: 100.0%
- Total number of restraints: 1343
- Weight of restraints: 1.0 (1343)
- Potential type of restraints: square-well-parabolic (1343)
- Range of distance target values: 2.09, 4.89 (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

Keywords DNA biding protein, H-NS, Xylella fastidiosa

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Found 1 Document (0.666 seconds)

BMRB: 15314

Sample #1

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Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. HNS79c monomer, : 1 : 5 entities Detail

Experiments performed 14 experiments Detail

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NMR combined restraints 3 contents Detail