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Found 1 Document (0.685 seconds)

BMRB: 16147

2MMO

NMR assignments of oxidised thioredoxin from Plasmodium falciparum

Authors

Munte, C.E., Katja, B., Rolf, S.H., Hans, K.R.

Assembly

Trx

Entity

1. Trx (polymer, Thiol state: free and disulfide bound), 115 monomers, 12999.58 Da Detail

MRGSHHHHHH GSVKIVTSQS EFDSIISQNE LVIVDFFAEW CGPCKRIAPF YEECSKTYTK MVFIKVDVDE VSEVTEKENI TSMPTFKVYK NGSSVDTLLG ANDSALKQLI EKYAA

Formula weight

12999.58 Da

Entity Connection

disulfide 1 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS41:SG	1:CYS44:SG

Source organism

Plasmodium falciparum

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 93.0 %, Completeness: 87.0 %, Completeness (bb): 90.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	87.0 % (1167 of 1341)	90.7 % (627 of 691)	82.1 % (435 of 530)	87.5 % (105 of 120)
Backbone	90.9 % (622 of 684)	89.7 % (208 of 232)	91.2 % (310 of 340)	92.9 % (104 of 112)
Sidechain	84.4 % (647 of 767)	91.3 % (419 of 459)	75.7 % (227 of 300)	12.5 % (1 of 8)
Aromatic	43.8 % (56 of 128)	79.7 % (51 of 64)	7.9 % (5 of 63)	0.0 % (0 of 1)
Methyl	100.0 % (122 of 122)	100.0 % (61 of 61)	100.0 % (61 of 61)

1. Trx

MRGSHHHHHH GSVKIVTSQS EFDSIISQNE LVIVDFFAEW CGPCKRIAPF YEECSKTYTK MVFIKVDVDE VSEVTEKENI TSMPTFKVYK NGSSVDTLLG ANDSALKQLI EKYAA

Show sample condition

Sample #1

Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	Trx	[U-100% 13C; U-100% 15N]	1 mM
2	potassium phosphate	natural abundance	10 mM
3	DSS	natural abundance	0.1 mM
4	sodium azide	natural abundance	1 mM

Sample #2

Solvent system 92% H2O / 8% D2O, Pressure 1 atm, Temperature 293 K, pH 7.0

#	Name	Isotope labeling	Concentration
5	Trx	[U-100% 13C; U-100% 15N]	1 mM
6	potassium phosphate	natural abundance	10 mM
7	DSS	natural abundance	0.1 mM
8	sodium azide	natural abundance	1 mM
9	D2O	natural abundance	8 %

Sample #3

Solvent system 92% H2O / 8% D2O, Pressure 1 atm, Temperature 293 K, pH 7.0

#	Name	Isotope labeling	Concentration
10	Trx	natural abundance	1 mM
11	potassium phosphate	natural abundance	10 mM
12	DSS	natural abundance	0.1 mM
13	sodium azide	natural abundance	1 mM
14	D2O	natural abundance	8 %

LACS Plot; CA

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

Referencing offset: 0.41 ppm, Outliers: 2 Detail

LACS Plot; CB

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

Referencing offset: 0.41 ppm, Outliers: 2 Detail

LACS Plot; HA

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

Referencing offset: -0.05 ppm, Outliers: 2 Detail

LACS Plot; CO

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

Referencing offset: 0.27 ppm, Outliers: 4 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 2MMO, Strand ID: A Detail

Release date

2009-05-12

Citation

NMR assignments of oxidised thioredoxin from Plasmodium falciparum
Munte, C., Becker, K., Schirmer, R., Kalbitzer, H.
Biomol. NMR Assign. (2009), 3, 159-161, PubMed 19888680 , DOI 10.1007/s12104-009-9163-7 , Abstract

Related entities 1. Trx, : 1 : 1 : 232 entities Detail

Interaction partners 1. Trx, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 5 experiments Detail

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_16147_2mmo.nef
Input source #2: Coordindates	2mmo.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
A:30:CYS:SG	A:33:CYS:SG	unknown	oxidized 9.5%, reduced 90.5%, CA 63.05, CB 34.07 ppm	2.031

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
SVKIVTSQSEFDSIISQNELVIVDFFAEWCGPCKRIAPFYEECSKTYTKMVFIKVDVDEVSEVTEKENITSMPTFKVYKNGSSVDTLLGANDSALKQLIE
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
SVKIVTSQSEFDSIISQNELVIVDFFAEWCGPCKRIAPFYEECSKTYTKMVFIKVDVDEVSEVTEKENITSMPTFKVYKNGSSVDTLLGANDSALKQLIE

----
KYAA
||||
KYAA

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	104	0	0	100.0

Content subtype: combined_16147_2mmo.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	1		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1160		100.0 (chain: A, length: 104)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	2666 (1)	noe	100.0 (chain: A, length: 104)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	449 (1)	undefined	86.5 (chain: A, length: 104)
3	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	26 (1)	undefined	12.5 (chain: A, length: 104)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_6	OK	182 (182)	.	98.1 (chain: A, length: 104)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 104, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 636
  - ¹³C chemical shifts: 423
  - ¹⁵N chemical shifts: 101
- 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)
44	SER	HG	5.78
49	LYS	HZ1	7.83
49	LYS	HZ2	7.83
49	LYS	HZ3	7.83
71	SER	HG	5.48
74	THR	HG1	5.46

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	629	625	99.4
¹³C chemical shifts	483	423	87.6
¹⁵N chemical shifts	110	101	91.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	208	206	99.0
¹³C chemical shifts	208	203	97.6
¹⁵N chemical shifts	101	101	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	421	419	99.5
¹³C chemical shifts	275	220	80.0
¹⁵N chemical shifts	9	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	63	63	100.0
¹³C chemical shifts	63	61	96.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	52	51	98.1
¹³C chemical shifts	51	0	0.0
¹⁵N chemical shifts	1	0	0.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 104, Sequence coverage: 100.0%
- Total number of restraints: 2659
- Weight of restraints: 1.0 (2659)
- Potential type of restraints: square-well-parabolic (2659)
- Range of distance target values: 2.0, 7.35 (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: undefined
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 104, Sequence coverage: 86.5%
  - Total number of restraints: 445
  - Weight of restraints: 1.0 (445)
  - Potential type of restraints: square-well-parabolic (445)
  - Range of distance target values: 20.0, 20.0 (Å)
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map
  - Saveframe: CNS/XPLOR_distance_constraints_4
    - Status: Warning
    - Experiment type: undefined
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 104, Sequence coverage: 12.5%
    - Total number of restraints: 26
    - Weight of restraints: 1.0 (26)
    - Potential type of restraints: square-well-parabolic (26)
    - Range of distance target values: 2.94, 20.0 (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_6
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 104, Sequence coverage: 98.1%
- Total number of restraints: 182
- Total number of restraints per polymer type: 182
- Weight of restraints: 1.0 (182)
- Potential type of restraints: square-well-parabolic (182)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

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Found 1 Document (0.685 seconds)

BMRB: 16147

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Trx, : 1 : 1 : 232 entities Detail

Interaction partners 1. Trx, : 1 interactors Detail

Experiments performed 5 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 6 contents Detail