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Found 1 Document (1.095 seconds)

BMRB: 18003

2LKP

solution structure of apo-NmtR

Authors

Lee, C., Giedroc, D.

Assembly

apo-NmtR

Entity

1. apo-NmtR (polymer, Thiol state: not present), 119 monomers, 12704.19 × 2 Da Detail

GHGVEGRNRP SAPLDSQAAA QVASTLQALA TPSRLMILTQ LRNGPLPVTD LAEAIGMEQS AVSHQLRVLR NLGLVVGDRA GRSIVYSLYD THVAQLLDEA IYHSEHLHLG LSDRHPSAG

Total weight

25408.38 Da

Max. entity weight

12704.19 Da

Source organism

Mycobacterium tuberculosis

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete1

Sequence coverage: 97.5 %, Completeness: 81.6 %, Completeness (bb): 91.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	81.6 % (1058 of 1297)	79.3 % (528 of 666)	83.3 % (423 of 508)	87.0 % (107 of 123)
Backbone	91.9 % (645 of 702)	88.0 % (213 of 242)	93.7 % (325 of 347)	94.7 % (107 of 113)
Sidechain	72.6 % (511 of 704)	73.6 % (312 of 424)	73.7 % (199 of 270)	0.0 % (0 of 10)
Aromatic	11.5 % (6 of 52)	15.4 % (4 of 26)	7.7 % (2 of 26)
Methyl	86.4 % (140 of 162)	95.1 % (77 of 81)	77.8 % (63 of 81)

1. entity

GHGVEGRNRP SAPLDSQAAA QVASTLQALA TPSRLMILTQ LRNGPLPVTD LAEAIGMEQS AVSHQLRVLR NLGLVVGDRA GRSIVYSLYD THVAQLLDEA IYHSEHLHLG LSDRHPSAG

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	apo-NmtR	[U-13C; U-15N]	0.5 ~ 1.0 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 310 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
4	apo-NmtR	[U-13C; U-15N]		0.5 ~ 1.0 mM
5	D2O	natural abundance		100 %

Chem. Shift Complete2

Sequence coverage: 91.6 %, Completeness: 59.3 %, Completeness (bb): 71.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	59.3 % (1538 of 2594)	56.4 % (751 of 1332)	56.1 % (570 of 1016)	88.2 % (217 of 246)
Backbone	71.6 % (1005 of 1404)	71.9 % (348 of 484)	63.7 % (442 of 694)	95.1 % (215 of 226)
Sidechain	46.6 % (656 of 1408)	47.2 % (400 of 848)	47.0 % (254 of 540)	10.0 % (2 of 20)
Aromatic	5.8 % (6 of 104)	7.7 % (4 of 52)	3.8 % (2 of 52)
Methyl	58.0 % (188 of 324)	64.2 % (104 of 162)	51.9 % (84 of 162)

1. entity

GHGVEGRNRP SAPLDSQAAA QVASTLQALA TPSRLMILTQ LRNGPLPVTD LAEAIGMEQS AVSHQLRVLR NLGLVVGDRA GRSIVYSLYD THVAQLLDEA IYHSEHLHLG LSDRHPSAG

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	apo-NmtR	[U-13C; U-15N]	0.5 ~ 1.0 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 310 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
4	apo-NmtR	[U-13C; U-15N]		0.5 ~ 1.0 mM
5	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: 0.07 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: 0.07 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: 0.1 ppm, Outliers: 1 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: 0.01 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 19 models in PDB: 2LKP, Strand ID: A, B Detail

Release date

2012-03-08

Citation

Solution structure of Mycobacterium tuberculosis NmtR in the apo state: insights into Ni(II)-mediated allostery
Lee, C., Chakravorty, D.K., Chang, F., Reyes-Caballero, H., Ye, Y., Merz, K.M., Giedroc, D.P.
Biochemistry (2012), 51, 2619-2629, PubMed 22394357 , DOI 10.1021/bi3001402 , Abstract

Entries sharing articles Swiss-Prot: 1 entries Detail

Swiss-Prot: O69711 released on 2012-10-03
Title NMTR_MYCTU Entity HTH-type transcriptional regulator NmtR

Related entities 1. apo-NmtR, : 1 : 2 : 23 entities Detail

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	apo-NmtR	[U-13C; U-15N]	0.5 ~ 1.0 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

2 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 310 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
4	apo-NmtR	[U-13C; U-15N]		0.5 ~ 1.0 mM
5	D2O	natural abundance		100 %

3 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	apo-NmtR	[U-13C; U-15N]	0.5 ~ 1.0 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

4 3D C(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	apo-NmtR	[U-13C; U-15N]	0.5 ~ 1.0 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

5 3D HNCO

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	apo-NmtR	[U-13C; U-15N]	0.5 ~ 1.0 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

6 3D HNCA

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	apo-NmtR	[U-13C; U-15N]	0.5 ~ 1.0 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

7 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	apo-NmtR	[U-13C; U-15N]	0.5 ~ 1.0 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

8 3D HCCH-TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 310 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
4	apo-NmtR	[U-13C; U-15N]		0.5 ~ 1.0 mM
5	D2O	natural abundance		100 %

9 3D 1H-15N NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	apo-NmtR	[U-13C; U-15N]	0.5 ~ 1.0 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

10 3D 1H-15N TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	apo-NmtR	[U-13C; U-15N]	0.5 ~ 1.0 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

11 3D 1H-13C NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 310 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
4	apo-NmtR	[U-13C; U-15N]		0.5 ~ 1.0 mM
5	D2O	natural abundance		100 %

NMR combined restraints 7 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_18003_2lkp.nef
Input source #2: Coordindates	2lkp.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-
GHGVEGRNRPSAPLDSQAAAQVASTLQALATPSRLMILTQLRNGPLPVTDLAEAIGMEQSAVSHQLRVLRNLGLVVGDRAGRSIVYSLYDTHVAQLLDEA
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GHGVEGRNRPSAPLDSQAAAQVASTLQALATPSRLMILTQLRNGPLPVTDLAEAIGMEQSAVSHQLRVLRNLGLVVGDRAGRSIVYSLYDTHVAQLLDEA
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

------110-------120
IYHSEHLHLGLSDRHPSAG
|||||||||||||||||||
IYHSEHLHLGLSDRHPSAG
-------110---------

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

-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220
GHGVEGRNRPSAPLDSQAAAQVASTLQALATPSRLMILTQLRNGPLPVTDLAEAIGMEQSAVSHQLRVLRNLGLVVGDRAGRSIVYSLYDTHVAQLLDEA
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GHGVEGRNRPSAPLDSQAAAQVASTLQALATPSRLMILTQLRNGPLPVTDLAEAIGMEQSAVSHQLRVLRNLGLVVGDRAGRSIVYSLYDTHVAQLLDEA
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

-------230---------
IYHSEHLHLGLSDRHPSAG
|||||||||||||||||||
IYHSEHLHLGLSDRHPSAG
-------110---------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	119	0	0	100.0
B	B	119	0	0	100.0

Content subtype: combined_18003_2lkp.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1029		97.5 (chain: A, length: 119)
2	Assigned chemical shifts	assigned_chem_shift_list_2	Warning	286		90.8 (chain: A, length: 119)
1	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	1366 (1)	noe	92.4 (chain: A, length: 119), 92.4 (chain: B, length: 119)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	192 (1)	hbond	56.3 (chain: A, length: 119), 56.3 (chain: B, length: 119)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	284 (284)	.	71.4 (chain: A, length: 119), 71.4 (chain: B, length: 119)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_5	OK	92 (92)	.	38.7 (chain: A, length: 119), 38.7 (chain: B, length: 119)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 119, Sequence coverage: 97.5%
- Total number of assignments
  - ¹H chemical shifts: 509
  - ¹³C chemical shifts: 412
  - ¹⁵N chemical shifts: 108
- 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
Saveframe: assigned_chem_shift_list_2
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 119, Sequence coverage: 90.8%
- Total number of assignments
  - ¹H chemical shifts: 108
  - ¹⁵N chemical shifts: 108
  - ¹³C chemical shifts: 70
- Completeness of assignments
  - Entity_assemble_ID: A
- 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	666	509	76.4
¹³C chemical shifts	508	412	81.1
¹⁵N chemical shifts	132	108	81.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	242	217	89.7
¹³C chemical shifts	238	223	93.7
¹⁵N chemical shifts	113	108	95.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	424	292	68.9
¹³C chemical shifts	270	189	70.0
¹⁵N chemical shifts	19	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	83	77	92.8
¹³C chemical shifts	83	61	73.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	26	0	0.0
¹³C chemical shifts	26	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	666	108	16.2
¹⁵N chemical shifts	132	108	81.8
¹³C chemical shifts	508	70	13.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	242	108	44.6
¹⁵N chemical shifts	113	108	95.6
¹³C chemical shifts	238	70	29.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	424	0	0.0
¹⁵N chemical shifts	19	0	0.0
¹³C chemical shifts	270	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	83	0	0.0
¹³C chemical shifts	83	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	26	0	0.0
¹³C chemical shifts	26	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: 119, Sequence coverage: 92.4%
  - Entity_assembly_ID: B, Chain length: 119, Sequence coverage: 92.4%
- Total number of restraints: 1362
- Weight of restraints: 1.0 (1362)
- Potential type of restraints: square-well-parabolic (1362)
- Range of distance target values: 1.35, 3.0 (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: 119, Sequence coverage: 56.3%
    - Entity_assembly_ID: B, Chain length: 119, Sequence coverage: 56.3%
  - Total number of restraints: 192
  - Weight of restraints: 1.0 (192)
  - Potential type of restraints: square-well-parabolic (192)
  - Range of distance target values: 1.0, 1.5 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
  - 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: 119, Sequence coverage: 71.4%
  - Entity_assembly_ID: B, Chain length: 119, Sequence coverage: 71.4%
- Total number of restraints: 284
- Total number of restraints per polymer type: 284
- Weight of restraints: 1.0 (284)
- Potential type of restraints: square-well-parabolic (284)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_5
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 119, Sequence coverage: 38.7%
  - Entity_assembly_ID: B, Chain length: 119, Sequence coverage: 38.7%
- Total number of restraints: 92
- Potential type of restraints: undefined (92)
- Range of observed RDC values: 100.0, -100.0 (Hz)
- RDC restraints per residue

Keywords DNA binding protein, Mycobacterium tuberculosis, Ni(II) binding protein, synmetric homodimer

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Found 1 Document (1.095 seconds)

BMRB: 18003

Sample #1

Sample #2

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Entries sharing articles Swiss-Prot: 1 entries Detail

Related entities 1. apo-NmtR, : 1 : 2 : 23 entities Detail

Experiments performed 11 experiments Detail

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NMR combined restraints 7 contents Detail