BMRBj - BMREntryMaster

Found 1 Document (0.701 seconds)

BMRB: 30334

6AP5

H, 13C, and 15N Chemical Shift Assignments and structure of Thioredoxin from Mycobacterium thermoresistibile ATCC 19527 and NCTC 10409

Authors

Tang, C.T., Yang, F.Y., Varani, G.V., Seattle Structural Genomics Center for Infectious Disease (SSGCID), S.

Assembly

Thioredoxin

Entity

1. Thioredoxin (polymer, Thiol state: all free), 115 monomers, 12490.24 Da Detail

MAHHHHHHMS GTVTVTDSTF KTDVLDSDTP VLVDFWADWC GPCKMVAPVL EEIANEKSGT LKVAKLDVDA NPEAARDFQV VSIPTMILFK GGTPVKRIVG AKGKAALLRE IEDAL

Formula weight

12490.24 Da

Source organism

Mycolicibacterium thermoresistibile ATCC 19527

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 96.5 %, Completeness: 86.2 %, Completeness (bb): 94.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	86.2 % (1112 of 1290)	83.9 % (553 of 659)	87.0 % (450 of 517)	95.6 % (109 of 114)
Backbone	94.8 % (643 of 678)	95.7 % (221 of 231)	94.1 % (318 of 338)	95.4 % (104 of 109)
Sidechain	79.6 % (573 of 720)	77.6 % (332 of 428)	82.2 % (236 of 287)	100.0 % (5 of 5)
Aromatic	31.8 % (28 of 88)	31.8 % (14 of 44)	28.6 % (12 of 42)	100.0 % (2 of 2)
Methyl	88.7 % (133 of 150)	88.0 % (66 of 75)	89.3 % (67 of 75)

1. entity 1

MAHHHHHHMS GTVTVTDSTF KTDVLDSDTP VLVDFWADWC GPCKMVAPVL EEIANEKSGT LKVAKLDVDA NPEAARDFQV VSIPTMILFK GGTPVKRIVG AKGKAALLRE IEDAL

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 Pa, Temperature 298 K, pH 6.0, Details 1 mM [U-95% 13C; U-95% 15N] Thioredoxin, 100 mM sodium chloride, 25 mM sodium phosphate, 2 mM DTT, 10 % v/v D20, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	D20	natural abundance	10 % v/v
2	DTT	natural abundance	2 mM
3	Thioredoxin	[U-95% 13C; U-95% 15N]	1 mM
4	sodium chloride	natural abundance	100 mM
5	sodium phosphate	natural abundance	25 mM

Sample #2

Solvent system 100% D2O, Pressure 1 Pa, Temperature 298 K, pH 6.0, Details 1 mM [U-95% 13C; U-95% 15N] Thioredoxin, 100 mM sodium chloride, 25 mM sodium phosphate, 2 mM DTT, 100 % v/v D2O, 100% D2O

#	Name	Isotope labeling	Concentration
6	D2O	natural abundance	100 % v/v
7	DTT	natural abundance	2 mM
8	Thioredoxin	[U-95% 13C; U-95% 15N]	1 mM
9	sodium chloride	natural abundance	100 mM
10	sodium phosphate	natural abundance	25 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: -0.09 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: -0.09 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: -0.08 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: 0.06 ppm, Outliers: 4 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 6AP5, Strand ID: A Detail

Release date

2017-10-18

Citation

1H, 13C, and 15N Chemical Shift Assignments and structure of Thioredoxin from Mycobacterium thermoresistibile ATCC 19527 and NCTC 10409
Tang, C.T., Yang, F.Y., Varani, G.V.

Related entities 1. Thioredoxin, : 1 : 220 entities Detail

Experiments performed 7 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 Pa, Temperature 298 K, pH 6.0, Details 1 mM [U-95% 13C; U-95% 15N] Thioredoxin, 100 mM sodium chloride, 25 mM sodium phosphate, 2 mM DTT, 10 % v/v D20, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	D20	natural abundance	10 % v/v
2	DTT	natural abundance	2 mM
3	Thioredoxin	[U-95% 13C; U-95% 15N]	1 mM
4	sodium chloride	natural abundance	100 mM
5	sodium phosphate	natural abundance	25 mM

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 Pa, Temperature 298 K, pH 6.0, Details 1 mM [U-95% 13C; U-95% 15N] Thioredoxin, 100 mM sodium chloride, 25 mM sodium phosphate, 2 mM DTT, 100 % v/v D2O, 100% D2O

#	Name	Isotope labeling	Concentration
6	D2O	natural abundance	100 % v/v
7	DTT	natural abundance	2 mM
8	Thioredoxin	[U-95% 13C; U-95% 15N]	1 mM
9	sodium chloride	natural abundance	100 mM
10	sodium phosphate	natural abundance	25 mM

3 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	D20	natural abundance	10 % v/v
2	DTT	natural abundance	2 mM
3	Thioredoxin	[U-95% 13C; U-95% 15N]	1 mM
4	sodium chloride	natural abundance	100 mM
5	sodium phosphate	natural abundance	25 mM

4 3D HNCA

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	D20	natural abundance	10 % v/v
2	DTT	natural abundance	2 mM
3	Thioredoxin	[U-95% 13C; U-95% 15N]	1 mM
4	sodium chloride	natural abundance	100 mM
5	sodium phosphate	natural abundance	25 mM

5 3D HBHA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	D20	natural abundance	10 % v/v
2	DTT	natural abundance	2 mM
3	Thioredoxin	[U-95% 13C; U-95% 15N]	1 mM
4	sodium chloride	natural abundance	100 mM
5	sodium phosphate	natural abundance	25 mM

6 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
6	D2O	natural abundance	100 % v/v
7	DTT	natural abundance	2 mM
8	Thioredoxin	[U-95% 13C; U-95% 15N]	1 mM
9	sodium chloride	natural abundance	100 mM
10	sodium phosphate	natural abundance	25 mM

7 3D H(CCO)NH

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	D20	natural abundance	10 % v/v
2	DTT	natural abundance	2 mM
3	Thioredoxin	[U-95% 13C; U-95% 15N]	1 mM
4	sodium chloride	natural abundance	100 mM
5	sodium phosphate	natural abundance	25 mM

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Dihedral angle restraints	combined_30334_6ap5.nef
Input source #2: Coordindates	6ap5.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
MAHHHHHHMSGTVTVTDSTFKTDVLDSDTPVLVDFWADWCGPCKMVAPVLEEIANEKSGTLKVAKLDVDANPEAARDFQVVSIPTMILFKGGTPVKRIVG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MAHHHHHHMSGTVTVTDSTFKTDVLDSDTPVLVDFWADWCGPCKMVAPVLEEIANEKSGTLKVAKLDVDANPEAARDFQVVSIPTMILFKGGTPVKRIVG

-------110-----
AKGKAALLREIEDAL
|||||||||||||||
AKGKAALLREIEDAL

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_30334_6ap5.nef

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1098		94.8 (chain: A, length: 115)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	114 (114)	.	63.5 (chain: A, length: 115)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 115, Sequence coverage: 94.8%
- Total number of assignments
  - ¹H chemical shifts: 544
  - ¹³C chemical shifts: 443
  - ¹⁵N chemical shifts: 111
- 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	ASN	CG	175.965
79	GLN	CD	180.98

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	659	544	82.5
¹³C chemical shifts	517	441	85.3
¹⁵N chemical shifts	117	111	94.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	231	218	94.4
¹³C chemical shifts	230	210	91.3
¹⁵N chemical shifts	109	103	94.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	428	326	76.2
¹³C chemical shifts	287	231	80.5
¹⁵N chemical shifts	8	8	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	79	64	81.0
¹³C chemical shifts	79	65	82.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	44	12	27.3
¹³C chemical shifts	42	10	23.8
¹⁵N chemical shifts	2	2	100.0

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 115, Sequence coverage: 63.5%
- Total number of restraints: 114
- Total number of restraints per polymer type: 114
- Weight of restraints: 1.0 (114)
- Potential type of restraints: square-well-parabolic (114)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords SSGCID, STRUCTURAL PROTEIN, STRUCTURE FROM CYANA 3.97, Seattle Structural Genomics Center for Infectious Disease, Structural Genomics

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (0.701 seconds)

BMRB: 30334

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Thioredoxin, : 1 : 220 entities Detail

Experiments performed 7 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 3 contents Detail