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Found 1 Document (1.503 seconds)

BMRB: 5767

1ORL

1H NMR structure determination of Viscotoxin C1

Authors

Molinari, H., Romagnoli, S., Fogolari, F., Catalano, M., Urech, K., Giannattasio, M., Ragona, L.

Assembly

Viscotoxin C1

Entity

1. Viscotoxin C1 (polymer, Thiol state: all disulfide bound), 46 monomers, 4946.629 Da Detail

KSCCPNTTGR NIYNTCRFAG GSRERCAKLS GCKIISASTC PSDYPK

Formula weight

4946.629 Da

Entity Connection

disulfide 3 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS3:SG	1:CYS40:SG
2	disulfide	sing	1:CYS4:SG	1:CYS32:SG
3	disulfide	sing	1:CYS16:SG	1:CYS26:SG

Source organism

Viscum album

Exptl. method

NMR

Refine. method

DYANA was employed for structure determination

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 90.9 %, Completeness (bb): 98.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H
All	90.9 % (239 of 263)	90.9 % (239 of 263)
Backbone	98.9 % (92 of 93)	98.9 % (92 of 93)
Sidechain	86.5 % (147 of 170)	86.5 % (147 of 170)
Aromatic	46.2 % (6 of 13)	46.2 % (6 of 13)
Methyl	100.0 % (15 of 15)	100.0 % (15 of 15)

1. Cue2

KSCCPNTTGR NIYNTCRFAG GSRERCAKLS GCKIISASTC PSDYPK

Show sample condition

Sample

Pressure 1 atm, Temperature 285 K, pH 3.6

#	Name	Concentration
1	Cue2	0.7 mM
2	phosphate buffer	50 mM
3	H20	90 %
4	D2O	10 %

Protein Blocks Logo

Calculated from 10 models in PDB: 1ORL, Strand ID: A Detail

Release date

2003-04-10

Citation

NMR solution structure of viscotoxin C1 from Viscum album species Coloratum ohwi: toward a structure-function analysis of viscotoxins
Romagnoli, S., Fogolari, F., Catalano, M., Zetta, L., Schaller, G., Urech, K., Giannattasio, M., Ragona, L., Molinari, H.
Biochemistry (2003), 42, 12503-12510, PubMed 14580196 , DOI 10.1021/bi034762t , Abstract

Entries sharing articles Swiss-Prot: 1 entries Detail

Swiss-Prot: P83554 released on 2004-04-13
Title THNC_VISAL Entity Viscotoxin-C1

Related entities 1. Viscotoxin C1, : 1 : 1 : 6 : 62 entities Detail

Experiments performed 3 experiments Detail

#	Name	Concentration
5	Cue2	0.7 mM
6	phosphate buffer	50 mM
7	D2O	100 %

#	Name	Concentration
5	Cue2	0.7 mM
6	phosphate buffer	50 mM
7	D2O	100 %

#	Name	Concentration
5	Cue2	0.7 mM
6	phosphate buffer	50 mM
7	D2O	100 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_5767_1orl.nef
Input source #2: Coordindates	1orl.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:3:CYS:SG	A:40:CYS:SG	unknown	unknown	2.034
A:4:CYS:SG	A:32:CYS:SG	unknown	unknown	2.035
A:16:CYS:SG	A:26:CYS:SG	unknown	unknown	2.039

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------
KSCCPNTTGRNIYNTCRFAGGSRERCAKLSGCKIISASTCPSDYPK
||||||||||||||||||||||||||||||||||||||||||||||
KSCCPNTTGRNIYNTCRFAGGSRERCAKLSGCKIISASTCPSDYPK

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	46	0	0	100.0

Content subtype: combined_5767_1orl.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	system_Cue2	OK	3		No information
1	Assigned chemical shifts	chemical_shift_set_1	Warning	248		100.0 (chain: A, length: 46)
1	Distance restraints	Discover_distance_constraints_2	Warning	853 (1)	noe	100.0 (chain: A, length: 46)
2	Distance restraints	Discover_distance_constraints_3	OK	24 (1)	hbond	45.7 (chain: A, length: 46)
1	Dihedral angle restraints	Discover_dihedral_4	OK	18 (18)	.	60.9 (chain: A, length: 46)

Assigned chemical shifts

Saveframe: chemical_shift_set_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 46, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 248
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
1	LYS	HZ1	7.555
1	LYS	HZ2	7.555
1	LYS	HZ3	7.555
17	ARG	HH11	6.596
17	ARG	HH12	7.042
30	SER	HG	5.847
46	LYS	HZ1	7.611
46	LYS	HZ2	7.611
46	LYS	HZ3	7.611

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	263	239	90.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	93	92	98.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	170	147	86.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	15	15	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	13	6	46.2

Covalent bonds

Saveframe: system_Cue2
- Status: OK

Distance restraints

Saveframe: Discover_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 46, Sequence coverage: 100.0%
- Total number of restraints: 852
- Weight of restraints: 1.0 (852)
- Potential type of restraints: square-well-parabolic (852)
- Range of distance target values: 1.95, 5.05 (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: Discover_distance_constraints_3
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 46, Sequence coverage: 45.7%
  - Total number of restraints: 24
  - Weight of restraints: 1.0 (24)
  - Potential type of restraints: square-well-parabolic (24)
  - Range of distance target values: 1.9, 2.4 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: Discover_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 46, Sequence coverage: 60.9%
- Total number of restraints: 18
- Total number of restraints per polymer type: 18
- Weight of restraints: 1.0 (18)
- Potential type of restraints: square-well-parabolic (18)
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords beta-sheet, concentric motif of disulphide bridges, helix-turn-helix

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Found 1 Document (1.503 seconds)

BMRB: 5767

Sample

Entries sharing articles Swiss-Prot: 1 entries Detail

Related entities 1. Viscotoxin C1, : 1 : 1 : 6 : 62 entities Detail

Experiments performed 3 experiments Detail

Instrument

Sample #1

Sample #2

Instrument

Sample #1

Sample #2

Instrument

Sample #1

Sample #2

NMR combined restraints 5 contents Detail