BMRBj - BMREntryMaster

Found 1 Document (1.115 seconds)

BMRB: 30290

5VO7

NMR Assignment and Structure of Thioredoxin (Rv1471 ortholog) from Mycobacterium smegmatis ATCC 700084 / mc(2)155

Authors

Barnwal, R.P., Varani, G., Seattle Structural Genomics Center for Infectious Disease (SSGCID), S.

Assembly

Thioredoxin

Entity

1. Thioredoxin (polymer, Thiol state: all free), 110 monomers, 11623.25 Da Detail

MSEDSATVAV TDDSFSTDVL GSSKPVLVDF WATWCGPCKM VAPVLEEIAA EKGDQLTVAK IDVDANPATA RDFQVVSIPT MILFKDGAPV KRIVGAKGKA ALLRELSDAL

Formula weight

11623.25 Da

Source organism

Mycolicibacterium smegmatis

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 88.8 %, Completeness (bb): 98.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	88.8 % (1073 of 1209)	84.4 % (520 of 616)	92.6 % (448 of 484)	96.3 % (105 of 109)
Backbone	98.8 % (640 of 648)	97.3 % (214 of 220)	99.7 % (323 of 324)	99.0 % (103 of 104)
Sidechain	80.8 % (537 of 665)	77.3 % (306 of 396)	86.7 % (229 of 264)	40.0 % (2 of 5)
Aromatic	21.9 % (14 of 64)	43.8 % (14 of 32)	0.0 % (0 of 30)	0.0 % (0 of 2)
Methyl	96.7 % (147 of 152)	93.4 % (71 of 76)	100.0 % (76 of 76)

1. entity 1

MSEDSATVAV TDDSFSTDVL GSSKPVLVDF WATWCGPCKM VAPVLEEIAA EKGDQLTVAK IDVDANPATA RDFQVVSIPT MILFKDGAPV KRIVGAKGKA ALLRELSDAL

Show sample condition

Sample

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details 1.1 mM [U-99% 13C; U-99% 15N] Thioredoxin (Rv1471 ortholog) from Mycobacterium smegmatis ATCC 700084 / mc(2)15513C, 93% H2O/7% D2O

#	Name	Isotope labeling	Type	Concentration
1	Thioredoxin (Rv1471 ortholog) from Mycobacterium smegmatis ATCC 700084 / mc(2)15513C	[U-99% 13C; U-99% 15N]		1.1 (±0.1) mM
2	NaCl	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: 1.81 ppm, Outliers: 6 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: 1.81 ppm, Outliers: 6 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: 2 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: 4 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 5VO7, Strand ID: A Detail

Release date

2017-05-30

Citation

Assignment and Structure of Thioredoxin (Rv1471 ortholog) type protein from Mycobacterium smegmatis ATCC 700084 / mc(2)155
Barnwal, R.P., Varani, G.

Related entities 1. Thioredoxin, : 1 : 231 entities Detail

Experiments performed 9 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AvanceII - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details 1.1 mM [U-99% 13C; U-99% 15N] Thioredoxin (Rv1471 ortholog) from Mycobacterium smegmatis ATCC 700084 / mc(2)15513C, 93% H2O/7% D2O

#	Name	Isotope labeling	Type	Concentration
1	Thioredoxin (Rv1471 ortholog) from Mycobacterium smegmatis ATCC 700084 / mc(2)15513C	[U-99% 13C; U-99% 15N]		1.1 (±0.1) mM
2	NaCl	natural abundance		100 mM

2 2D 1H-13C HSQC

Instrument

Bruker AvanceII - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	Thioredoxin (Rv1471 ortholog) from Mycobacterium smegmatis ATCC 700084 / mc(2)15513C	[U-99% 13C; U-99% 15N]		1.1 (±0.1) mM
2	NaCl	natural abundance		100 mM

3 3D CBCA(CO)NH

Instrument

Bruker AvanceII - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	Thioredoxin (Rv1471 ortholog) from Mycobacterium smegmatis ATCC 700084 / mc(2)15513C	[U-99% 13C; U-99% 15N]		1.1 (±0.1) mM
2	NaCl	natural abundance		100 mM

4 3D HNCACB

Instrument

Bruker AvanceII - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	Thioredoxin (Rv1471 ortholog) from Mycobacterium smegmatis ATCC 700084 / mc(2)15513C	[U-99% 13C; U-99% 15N]		1.1 (±0.1) mM
2	NaCl	natural abundance		100 mM

5 3D HNCO

Instrument

Bruker AvanceII - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	Thioredoxin (Rv1471 ortholog) from Mycobacterium smegmatis ATCC 700084 / mc(2)15513C	[U-99% 13C; U-99% 15N]		1.1 (±0.1) mM
2	NaCl	natural abundance		100 mM

6 3D 1H-13C NOESY

Instrument

Bruker AvanceIII - 800 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	Thioredoxin (Rv1471 ortholog) from Mycobacterium smegmatis ATCC 700084 / mc(2)15513C	[U-99% 13C; U-99% 15N]		1.1 (±0.1) mM
2	NaCl	natural abundance		100 mM

7 3D 1H-15N NOESY

Instrument

Bruker AvanceIII - 800 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	Thioredoxin (Rv1471 ortholog) from Mycobacterium smegmatis ATCC 700084 / mc(2)15513C	[U-99% 13C; U-99% 15N]		1.1 (±0.1) mM
2	NaCl	natural abundance		100 mM

8 3D HBHA(CO)NH

Instrument

Bruker AvanceII - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	Thioredoxin (Rv1471 ortholog) from Mycobacterium smegmatis ATCC 700084 / mc(2)15513C	[U-99% 13C; U-99% 15N]		1.1 (±0.1) mM
2	NaCl	natural abundance		100 mM

9 3D HCCH-TOCSY

Instrument

Bruker AvanceII - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	Thioredoxin (Rv1471 ortholog) from Mycobacterium smegmatis ATCC 700084 / mc(2)15513C	[U-99% 13C; U-99% 15N]		1.1 (±0.1) mM
2	NaCl	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_30290_5vo7.nef
Input source #2: Coordindates	5vo7.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
MSEDSATVAVTDDSFSTDVLGSSKPVLVDFWATWCGPCKMVAPVLEEIAAEKGDQLTVAKIDVDANPATARDFQVVSIPTMILFKDGAPVKRIVGAKGKA
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MSEDSATVAVTDDSFSTDVLGSSKPVLVDFWATWCGPCKMVAPVLEEIAAEKGDQLTVAKIDVDANPATARDFQVVSIPTMILFKDGAPVKRIVGAKGKA

-------110
ALLRELSDAL
||||||||||
ALLRELSDAL

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	110	0	0	100.0

Content subtype: combined_30290_5vo7.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1076		100.0 (chain: A, length: 110)
1	Distance restraints	DYANA/DIANA_distance_constraints_5	Warning	1652 (1)	noe	100.0 (chain: A, length: 110)
2	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	24 (1)	hbond	5.5 (chain: A, length: 110)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_4	OK	1135 (1135)	.	100.0 (chain: A, length: 110)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 110, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 523
  - ¹³C chemical shifts: 448
  - ¹⁵N chemical shifts: 105
- 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)
55	GLN	CD	180.072
74	GLN	CD	180.929

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	616	523	84.9
¹³C chemical shifts	484	446	92.1
¹⁵N chemical shifts	112	105	93.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	220	219	99.5
¹³C chemical shifts	220	220	100.0
¹⁵N chemical shifts	104	103	99.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	396	304	76.8
¹³C chemical shifts	264	226	85.6
¹⁵N chemical shifts	8	2	25.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	79	69	87.3
¹³C chemical shifts	79	75	94.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	32	14	43.8
¹³C chemical shifts	30	0	0.0
¹⁵N chemical shifts	2	0	0.0

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_5
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 110, Sequence coverage: 100.0%
- Total number of restraints: 1652
- Weight of restraints: 1.0 (1652)
- Potential type of restraints: upper-bound-parabolic (1652)
- Range of distance target values: 2.31, 5.5 (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_2
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 110, Sequence coverage: 5.5%
  - Total number of restraints: 24
  - Weight of restraints: 1.0 (24)
  - Potential type of restraints: upper-bound-parabolic (24)
  - Range of distance target values: 1.8, 3.0 (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

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 110, Sequence coverage: 100.0%
- Total number of restraints: 1135
- Total number of restraints per polymer type: 1135
- Weight of restraints: 1.0 (1135)
- Potential type of restraints: square-well-parabolic (1135)
- Plot of Phi-Psi angle restraints
- Plot of Chi1-Chi2 angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords ELECTRON TRANSPORT, PROTEIN, PROTEIN NMR Thioredoxin Mycobacterium smegmatis, SSGCID, Seattle Structural Genomics Center for Infectious Disease, Structural Genomics

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Found 1 Document (1.115 seconds)

BMRB: 30290

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Thioredoxin, : 1 : 231 entities Detail

Experiments performed 9 experiments Detail

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NMR combined restraints 5 contents Detail