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BMRB: 17997

2LK6

Solution structure of the Cd(II) form of Desulforedoxin

Authors

Goodfellow, B.J., Tavares, P., Romao, M.J., Czaja, C., Rusnak, F., LeGall, J., Moura, I., Moura, J.JG.

Assembly

Cd(II) form of Desulforedoxin

Entity

1. Cd(II) form of Desulforedoxin, entity (polymer, Thiol state: unknown), 36 monomers, 3804.324 Da Detail

ANEGDVYKCE LCGQVVKVLE EGGGTLVCCG EDMVKQ

2. CD (non-polymer), 112.411 Da

Total weight

3916.7349 Da

Max. entity weight

3804.324 Da

Source organism

Desulfovibrio gigas

Exptl. method

solution NMR

Refine. method

distance geometry

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 98.5 %, Completeness (bb): 98.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H
All	98.5 % (194 of 197)	98.5 % (194 of 197)
Backbone	98.7 % (77 of 78)	98.7 % (77 of 78)
Sidechain	98.3 % (117 of 119)	98.3 % (117 of 119)
Aromatic	100.0 % (4 of 4)	100.0 % (4 of 4)
Methyl	95.0 % (19 of 20)	95.0 % (19 of 20)

1. entity

ANEGDVYKCE LCGQVVKVLE EGGGTLVCCG EDMVKQ

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0, Details pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	entity	natural abundance		2-4 mM

Protein Blocks Logo

Calculated from 18 models in PDB: 2LK6, Strand ID: A, B Detail

Release date

2011-11-01

Citation

The solution structure of desulforedoxin, a simple iron-sulfur protein - An NMR study of the zinc derivative
Goodfellow, B.J., Tavares, P., Romao, M., Czaja, C., Rusnak, F., LeGall, J., Moura, I., Moura, J.JG.
J. Biol. Inorg. Chem. (1996), 1, 341-354, PubMed , DOI 10.1007/s007750050062

Related entities 1. Cd(II) form of Desulforedoxin, entity, : 1 : 6 : 8 entities Detail

Experiments performed 3 experiments Detail

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_17997_2lk6.nef
Input source #2: Coordindates	2lk6.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	True (see coodinates for details)
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)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:12:CYS:SG	3:1:CD:CD	unknown	unknown	n/a
1:29:CYS:SG	3:1:CD:CD	unknown	unknown	n/a
2:12:CYS:SG	3:2:CD:CD	unknown	unknown	n/a
2:29:CYS:SG	3:2:CD:CD	unknown	unknown	n/a
1:28:CYS:SG	3:1:CD:CD	unknown	unknown	n/a
2:28:CYS:SG	3:2:CD:CD	unknown	unknown	n/a
1:9:CYS:SG	3:1:CD:CD	unknown	unknown	n/a
2:9:CYS:SG	3:2:CD:CD	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
C	1	CD	CADMIUM ION	None
C	2	CD	CADMIUM ION	None

Sequence alignments

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

--------10--------20--------30------
ANEGDVYKCELCGQVVKVLEEGGGTLVCCGEDMVKQ
||||||||||||||||||||||||||||||||||||
ANEGDVYKCELCGQVVKVLEEGGGTLVCCGEDMVKQ

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

--------10--------20--------30------
ANEGDVYKCELCGQVVKVLEEGGGTLVCCGEDMVKQ
||||||||||||||||||||||||||||||||||||
ANEGDVYKCELCGQVVKVLEEGGGTLVCCGEDMVKQ

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	36	0	0	100.0
B	B	36	0	0	100.0

Content subtype: combined_17997_2lk6.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	8		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	194		100.0 (chain: A, length: 36)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	1020 (1)	noe	100.0 (chain: A, length: 36), 100.0 (chain: B, length: 36)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 36, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 194
- 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	197	194	98.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	78	77	98.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	119	117	98.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	21	20	95.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	4	4	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 36, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 36, Sequence coverage: 100.0%
- Total number of restraints: 1020
- Weight of restraints: 1.0 (1020)
- Potential type of restraints: upper-bound-parabolic (1020)
- Range of distance target values: 2.0, 9.4 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
  - Chain_ID: C
    None
- Distance restraints on contact map

Keywords homo dimer

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Found 1 Document (0.618 seconds)

BMRB: 17997

Sample

Related entities 1. Cd(II) form of Desulforedoxin, entity, : 1 : 6 : 8 entities Detail

Experiments performed 3 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 3 contents Detail