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Found 1 Document (1.174 seconds)

BMRB: 30034

5IRD

Solution structure of Rv1466 from Mycobacterium tuberculosis, a protein associated with [Fe-S] complex assembly and repair - Seattle Structural Genomics Center for Infectious Disease target MytuD.17486.a

Authors

Buchko, G.W., Seattle Structural Genomics Center for Infectious Disease (SSGCID), S.

Assembly

Uncharacterized protein

Entity

1. Uncharacterized protein (polymer, Thiol state: all free), 119 monomers, 12681.97 Da Detail

GPGSMSETSA PAEELLADVE EAMRDVVDPE LGINVVDLGL VYGLDVQDGD EGTVALIDMT LTSAACPLTD VIEDQSRSAL VGSGLVDDIR INWVWNPPWG PDKITEDGRE QLRALGFTV

Formula weight

12681.97 Da

Source organism

Mycobacterium tuberculosis H37Ra

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 99.2 %, Completeness: 90.1 %, Completeness (bb): 94.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	90.1 % (1151 of 1277)	87.9 % (572 of 651)	91.5 % (462 of 505)	96.7 % (117 of 121)
Backbone	94.3 % (660 of 700)	93.8 % (228 of 243)	93.9 % (324 of 345)	96.4 % (108 of 112)
Sidechain	87.3 % (597 of 684)	84.3 % (344 of 408)	91.4 % (244 of 267)	100.0 % (9 of 9)
Aromatic	64.8 % (35 of 54)	66.7 % (18 of 27)	58.3 % (14 of 24)	100.0 % (3 of 3)
Methyl	91.3 % (146 of 160)	90.0 % (72 of 80)	92.5 % (74 of 80)

1. entity 1

GPGSMSETSA PAEELLADVE EAMRDVVDPE LGINVVDLGL VYGLDVQDGD EGTVALIDMT LTSAACPLTD VIEDQSRSAL VGSGLVDDIR INWVWNPPWG PDKITEDGRE QLRALGFTV

Show sample condition

Sample #1

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 (±0.5) K, pH 7.0 (±0.2), Details 1.0 mM [U-13C; U-15N] Rv1466, 100 mM sodium chloride, 20 mM TRIS, 1 mM DTT, 93% H2O/7% D2O

#	Name	Isotope labeling	Concentration
1	DTT	natural abundance	1 mM
2	Rv1466	[U-13C; U-15N]	1.0 (±0.2) mM
3	TRIS	natural abundance	20 mM
4	sodium chloride	natural abundance	100 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 293 (±0.5) K, pH 7.0 (±0.2), Details 0.5 mM [U-15N] Rv1466, 100 mM sodium chloride, 20 mM TRIS, 1 mM DTT, 100% D2O

#	Name	Isotope labeling	Concentration
5	DTT	natural abundance	1 mM
6	Rv1466	[U-15N]	0.5 mM
7	TRIS	natural abundance	20 mM
8	sodium chloride	natural abundance	100 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: 0.11 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: 0.11 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: -0.04 ppm, Outliers: 3 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: 0.32 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 5IRD, Strand ID: A Detail

Release date

2016-05-22

Citation

Solution structure of Rv1466, a Mycobacterium tuberculosis protein associated with [Fe-S] cluster assembly and repair
Buchko, G.W., Hewitt, S.N., Van Voorhis, W., Myler, P.J.

Related entities 1. Uncharacterized protein, : 1 : 1 : 9 entities Detail

Experiments performed 13 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian VXRS - 750 MHz

Sample

State anisotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 (±0.5) K, pH 7.0 (±0.2), Details 1.0 mM [U-13C; U-15N] Rv1466, 100 mM sodium chloride, 20 mM TRIS, 1 mM DTT, 93% H2O/7% D2O

#	Name	Isotope labeling	Concentration
1	DTT	natural abundance	1 mM
2	Rv1466	[U-13C; U-15N]	1.0 (±0.2) mM
3	TRIS	natural abundance	20 mM
4	sodium chloride	natural abundance	100 mM

2 2D 1H-13C HSQC aliphatic

Instrument

Varian VXRS - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DTT	natural abundance	1 mM
2	Rv1466	[U-13C; U-15N]	1.0 (±0.2) mM
3	TRIS	natural abundance	20 mM
4	sodium chloride	natural abundance	100 mM

3 2D 1H-13C HSQC aromatic

Instrument

Varian VXRS - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DTT	natural abundance	1 mM
2	Rv1466	[U-13C; U-15N]	1.0 (±0.2) mM
3	TRIS	natural abundance	20 mM
4	sodium chloride	natural abundance	100 mM

4 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DTT	natural abundance	1 mM
2	Rv1466	[U-13C; U-15N]	1.0 (±0.2) mM
3	TRIS	natural abundance	20 mM
4	sodium chloride	natural abundance	100 mM

5 3D CBCA(CO)NH

Instrument

Varian VXRS - 750 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DTT	natural abundance	1 mM
2	Rv1466	[U-13C; U-15N]	1.0 (±0.2) mM
3	TRIS	natural abundance	20 mM
4	sodium chloride	natural abundance	100 mM

6 3D H(CCO)NH

Instrument

Varian VXRS - 750 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DTT	natural abundance	1 mM
2	Rv1466	[U-13C; U-15N]	1.0 (±0.2) mM
3	TRIS	natural abundance	20 mM
4	sodium chloride	natural abundance	100 mM

7 3D HNCO

Instrument

Varian VXRS - 750 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DTT	natural abundance	1 mM
2	Rv1466	[U-13C; U-15N]	1.0 (±0.2) mM
3	TRIS	natural abundance	20 mM
4	sodium chloride	natural abundance	100 mM

8 Deuterium exchange

Instrument

Varian VXRS - 750 MHz

Sample

State anisotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 (±0.5) K, pH 7.0 (±0.2), Details 0.5 mM [U-15N] Rv1466, 100 mM sodium chloride, 20 mM TRIS, 1 mM DTT, 100% D2O

#	Name	Isotope labeling	Concentration
5	DTT	natural abundance	1 mM
6	Rv1466	[U-15N]	0.5 mM
7	TRIS	natural abundance	20 mM
8	sodium chloride	natural abundance	100 mM

9 2D Delta

Instrument

Varian VXRS - 750 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DTT	natural abundance	1 mM
2	Rv1466	[U-13C; U-15N]	1.0 (±0.2) mM
3	TRIS	natural abundance	20 mM
4	sodium chloride	natural abundance	100 mM

10 3D C(CO)NH

Instrument

Varian INOVA - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DTT	natural abundance	1 mM
2	Rv1466	[U-13C; U-15N]	1.0 (±0.2) mM
3	TRIS	natural abundance	20 mM
4	sodium chloride	natural abundance	100 mM

11 3D 1H-13C NOESY aliphatic

Instrument

Varian VXRS - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DTT	natural abundance	1 mM
2	Rv1466	[U-13C; U-15N]	1.0 (±0.2) mM
3	TRIS	natural abundance	20 mM
4	sodium chloride	natural abundance	100 mM

12 3D 1H-15N NOESY

Instrument

Varian VXRS - 750 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DTT	natural abundance	1 mM
2	Rv1466	[U-13C; U-15N]	1.0 (±0.2) mM
3	TRIS	natural abundance	20 mM
4	sodium chloride	natural abundance	100 mM

13 3D 1H-13C NOESY aromatic

Instrument

Varian VXRS - 750 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DTT	natural abundance	1 mM
2	Rv1466	[U-13C; U-15N]	1.0 (±0.2) mM
3	TRIS	natural abundance	20 mM
4	sodium chloride	natural abundance	100 mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30034_5ird.nef
Input source #2: Coordindates	5ird.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
GPGSMSETSAPAEELLADVEEAMRDVVDPELGINVVDLGLVYGLDVQDGDEGTVALIDMTLTSAACPLTDVIEDQSRSALVGSGLVDDIRINWVWNPPWG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GPGSMSETSAPAEELLADVEEAMRDVVDPELGINVVDLGLVYGLDVQDGDEGTVALIDMTLTSAACPLTDVIEDQSRSALVGSGLVDDIRINWVWNPPWG

-------110---------
PDKITEDGREQLRALGFTV
|||||||||||||||||||
PDKITEDGREQLRALGFTV

Chain assignments

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

Content subtype: combined_30034_5ird.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1107		96.6 (chain: A, length: 119)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	1377 (1)	noe	92.4 (chain: A, length: 119)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	76 (1)	hbond	44.5 (chain: A, length: 119)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	158 (158)	.	84.0 (chain: A, length: 119)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 119, Sequence coverage: 96.6%
- Total number of assignments
  - ¹H chemical shifts: 553
  - ¹³C chemical shifts: 439
  - ¹⁵N chemical shifts: 115
- 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)
90	ARG	NH1	73.82

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	651	553	84.9
¹³C chemical shifts	505	439	86.9
¹⁵N chemical shifts	126	114	90.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	243	223	91.8
¹³C chemical shifts	238	205	86.1
¹⁵N chemical shifts	112	105	93.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	408	330	80.9
¹³C chemical shifts	267	234	87.6
¹⁵N chemical shifts	14	9	64.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	83	75	90.4
¹³C chemical shifts	83	76	91.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	27	14	51.9
¹³C chemical shifts	24	10	41.7
¹⁵N chemical shifts	3	3	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 119, Sequence coverage: 92.4%
- Total number of restraints: 1377
- Weight of restraints: 1.0 (1377)
- Potential type of restraints: square-well-parabolic (1377)
- Range of distance target values: 2.33, 4.05 (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: CNS/XPLOR_distance_constraints_3
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 119, Sequence coverage: 44.5%
  - Total number of restraints: 76
  - Weight of restraints: 1.0 (76)
  - Potential type of restraints: square-well-parabolic (76)
  - Range of distance target values: 1.9, 2.85 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 119, Sequence coverage: 84.0%
- Total number of restraints: 158
- Total number of restraints per polymer type: 158
- Weight of restraints: 1.0 (158)
- Potential type of restraints: square-well-parabolic (158)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords SSGCID, Seattle Structural Genomics Center for Infectious Disease, Structural Genomics, TB, [Fe-S] complexes, infectious disease

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Found 1 Document (1.174 seconds)

BMRB: 30034

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Uncharacterized protein, : 1 : 1 : 9 entities Detail

Experiments performed 13 experiments Detail

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NMR combined restraints 5 contents Detail