BMRBj - BMREntryMaster

Found 1 Document (0.733 seconds)

BMRB: 15801

2K4J

ArsR DNA Binding Domain

Authors

Gupta, S.S., Cover, T.L., Krezel, A.M.

Assembly

ArsR

Entity

1. ArsR (polymer, Thiol state: not present), 115 monomers, 13277.82 Da Detail

MRGSHHHHHH GSEEVSEPGD ANIFRVDKDS REVYMHEKKL DLTRAEYEIL SLLISKKGYV FSRESIAIES ESINPESSNK SIDVIIGRLR SKIEKNPKQP QYIISVRGIG YKLEY

Formula weight

13277.82 Da

Source organism

Helicobacter pylori

Exptl. method

Refine. method

torsion angle dynamics, molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 93.0 %, Completeness: 73.8 %, Completeness (bb): 77.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	73.8 % (1013 of 1373)	78.0 % (565 of 724)	64.8 % (345 of 532)	88.0 % (103 of 117)
Backbone	77.1 % (526 of 682)	89.7 % (209 of 233)	63.6 % (215 of 338)	91.9 % (102 of 111)
Sidechain	72.7 % (581 of 799)	72.5 % (356 of 491)	74.2 % (224 of 302)	16.7 % (1 of 6)
Aromatic	14.6 % (14 of 96)	29.2 % (14 of 48)	0.0 % (0 of 48)
Methyl	95.5 % (107 of 112)	94.6 % (53 of 56)	96.4 % (54 of 56)

1. ArsR

MRGSHHHHHH GSEEVSEPGD ANIFRVDKDS REVYMHEKKL DLTRAEYEIL SLLISKKGYV FSRESIAIES ESINPESSNK SIDVIIGRLR SKIEKNPKQP QYIISVRGIG YKLEY

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.6

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.5 mM
2	NaCl			0.5 M

LACS Plot; CA

Referencing offset: 0.15 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: 0.15 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: 0.06 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2K4J, Strand ID: A Detail

Release date

2009-02-08

Citation

Structural analysis of the DNA-binding domain of the Helicobacter pylori response regulator ArsR
Gupta, S.S., Borin, B.N., Cover, T.L., Krezel, A.M.
J. Biol. Chem. (2009), 284, 6536-6545, PubMed 19117956 , DOI 10.1074/jbc.M804592200 , Abstract

Related entities 1. ArsR, : 1 : 44 entities Detail

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.6

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.5 mM
2	NaCl			0.5 M

2 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.6

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.5 mM
2	NaCl			0.5 M

3 3D CBCANH

Instrument

Bruker Avance - 600 MHz cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.6

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.5 mM
2	NaCl			0.5 M

4 3D HCC-TOCSY

Instrument

Bruker Avance - 600 MHz cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.6

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.5 mM
2	NaCl			0.5 M

5 3D HHC-TOCSY

Instrument

Bruker Avance - 600 MHz cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.6

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.5 mM
2	NaCl			0.5 M

6 3D H(CC)(CO)NH

Instrument

Bruker Avance - 600 MHz cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.6

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.5 mM
2	NaCl			0.5 M

7 3D HCC(CO)NH

Instrument

Bruker Avance - 600 MHz cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.6

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.5 mM
2	NaCl			0.5 M

8 3D HBHA(CO)NH

Instrument

Bruker Avance - 600 MHz cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.6

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.5 mM
2	NaCl			0.5 M

9 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.6

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.5 mM
2	NaCl			0.5 M

10 3D 1H-13C NOESY

Instrument

Bruker Avance - 600 MHz cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.6

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.5 mM
2	NaCl			0.5 M

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_15801_2k4j.nef
Input source #2: Coordindates	2k4j.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
MRGSHHHHHHGSEEVSEPGDANIFRVDKDSREVYMHEKKLDLTRAEYEILSLLISKKGYVFSRESIAIESESINPESSNKSIDVIIGRLRSKIEKNPKQP
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MRGSHHHHHHGSEEVSEPGDANIFRVDKDSREVYMHEKKLDLTRAEYEILSLLISKKGYVFSRESIAIESESINPESSNKSIDVIIGRLRSKIEKNPKQP

-------110-----
QYIISVRGIGYKLEY
|||||||||||||||
QYIISVRGIGYKLEY

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	115	0	0	100.0

Content subtype: combined_15801_2k4j.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	980		91.3 (chain: A, length: 115)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	1633 (1)	noe	89.6 (chain: A, length: 115)
2	Distance restraints	DYANA/DIANA_distance_constraints_4	Warning	456 (1)	noe	78.3 (chain: A, length: 115)
3	Distance restraints	DYANA/DIANA_distance_constraints_3	OK	96 (1)	hbond	52.2 (chain: A, length: 115)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 115, Sequence coverage: 91.3%
- Total number of assignments
  - ¹H chemical shifts: 559
  - ¹³C chemical shifts: 321
  - ¹⁵N chemical shifts: 100
- 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_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 115, Sequence coverage: 89.6%
- Total number of restraints: 1633
- Weight of restraints: 1.0 (1633)
- Potential type of restraints: upper-bound-parabolic (1633)
- Range of distance target values: 2.46, 7.65 (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: DYANA/DIANA_distance_constraints_4
  - Status: Warning
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 115, Sequence coverage: 78.3%
  - Total number of restraints: 456
  - Weight of restraints: 1.0 (456)
  - Potential type of restraints: upper-bound-parabolic (456)
  - Range of distance target values: 2.89, 7.41 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map
  - Saveframe: DYANA/DIANA_distance_constraints_3
    - Status: OK
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 115, Sequence coverage: 52.2%
    - Total number of restraints: 96
    - Weight of restraints: 1.0 (96)
    - Potential type of restraints: upper-bound-parabolic (96)
    - Range of distance target values: 2.0, 3.0 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
    - Distance restraints on contact map

Keywords acid resistance, Helicobacter pylori, Response regulator