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Found 1 Document (0.691 seconds)

BMRB: 19700

2MJ0

Spatial structure of P33A mutant of non-conventional toxin WTX from Naja kaouthia

Authors

Paramonov, A.S., Shenkarev, Z.O., Lyukmanova, E.N.

Assembly

P33A mutant of non-conventional toxin WTX from Naja kaouthia

Entity

1. P33A mutant of non-conventional toxin WTX from Naja kaouthia (polymer, Thiol state: all disulfide bound), 66 monomers, 7729.154 Da Detail

MLTCLNCPEM FCGKFQICRN GEKICFKKLH QRRALSWRYI RGCADTCPVG KPYEMIECCS TDKCNR

Formula weight

7729.154 Da

Entity Connection

disulfide 5 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS4:SG	1:CYS25:SG
2	disulfide	sing	1:CYS7:SG	1:CYS12:SG
3	disulfide	sing	1:CYS18:SG	1:CYS43:SG
4	disulfide	sing	1:CYS47:SG	1:CYS58:SG
5	disulfide	sing	1:CYS59:SG	1:CYS64:SG

Source organism

Naja kaouthia

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 98.6 %, Completeness (bb): 99.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹⁵N
All	98.6 % (482 of 489)	98.6 % (414 of 420)	98.6 % (68 of 69)
Backbone	99.0 % (194 of 196)	99.2 % (132 of 133)	98.4 % (62 of 63)
Sidechain	98.3 % (288 of 293)	98.3 % (282 of 287)	100.0 % (6 of 6)
Aromatic	93.8 % (30 of 32)	93.5 % (29 of 31)	100.0 % (1 of 1)
Methyl	100.0 % (23 of 23)	100.0 % (23 of 23)

1. WTX[P33A]

MLTCLNCPEM FCGKFQICRN GEKICFKKLH QRRALSWRYI RGCADTCPVG KPYEMIECCS TDKCNR

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 3.0

#	Name	Isotope labeling	Concentration
1	WTX[P33A]	[U-99% 15N]	0.5 mM
2	H2O	natural abundance	95 %
3	D2O	[U-100% 2H]	5 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 313 K, pH 3.0

#	Name	Isotope labeling	Type	Concentration
4	WTX[P33A]	[U-99% 15N]		0.5 mM
5	D2O	[U-100% 2H]		100 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2MJ0, Strand ID: A Detail

Release date

2014-12-21

Related entities 1. P33A mutant of non-conventional toxin WTX from Naja kaouthia, : 1 : 1 : 111 entities Detail

Experiments performed 6 experiments Detail

NMR combined restraints 9 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19700_2mj0.nef
Input source #2: Coordindates	2mj0.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:103:CYS:SG	A:124:CYS:SG	unknown	unknown	1.956
A:103:CYS:SG	A:117:CYS:SG	unknown	unknown	2.599
A:106:CYS:SG	A:111:CYS:SG	unknown	unknown	1.889
A:117:CYS:SG	A:142:CYS:SG	unknown	unknown	1.977
A:146:CYS:SG	A:157:CYS:SG	unknown	unknown	1.934
A:158:CYS:SG	A:163:CYS:SG	unknown	unknown	2.017

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

100-----110-------120-------130-------140-------150-------160-----
MLTCLNCPEMFCGKFQICRNGEKICFKKLHQRRALSWRYIRGCADTCPVGKPYEMIECCSTDKCNR
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MLTCLNCPEMFCGKFQICRNGEKICFKKLHQRRALSWRYIRGCADTCPVGKPYEMIECCSTDKCNR
--------10--------20--------30--------40--------50--------60------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	66	0	0	100.0

Content subtype: combined_19700_2mj0.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	6		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	488		100.0 (chain: A, length: 66)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	524 (1)	noe	97.0 (chain: A, length: 66)
2	Distance restraints	DYANA/DIANA_distance_constraints_4	Warning	15 (1)	undefined	15.2 (chain: A, length: 66)
3	Distance restraints	DYANA/DIANA_distance_constraints_5	OK	52 (1)	noe	40.9 (chain: A, length: 66)
4	Distance restraints	DYANA/DIANA_distance_constraints_7	Warning	15 (1)	undefined	15.2 (chain: A, length: 66)
5	Distance restraints	DYANA/DIANA_distance_constraints_3	OK	40 (1)	hbond	39.4 (chain: A, length: 66)
6	Distance restraints	DYANA/DIANA_distance_constraints_6	Warning	40 (1)	hbond	39.4 (chain: A, length: 66)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_8	OK	158 (158)	.	98.5 (chain: A, length: 66)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 66, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 414
  - ¹⁵N chemical shifts: 74
- 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	420	414	98.6
¹⁵N chemical shifts	75	74	98.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	133	132	99.2
¹⁵N chemical shifts	63	62	98.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	287	282	98.3
¹⁵N chemical shifts	12	12	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	26	23	88.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	31	29	93.5
¹⁵N chemical shifts	1	1	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 66, Sequence coverage: 97.0%
- Total number of restraints: 524
- Weight of restraints: 1.0 (524)
- Potential type of restraints: upper-bound-parabolic (524)
- Range of distance target values: 1.51, 5.2 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: DYANA/DIANA_distance_constraints_4
  - Status: Warning
  - Experiment type: undefined
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 66, Sequence coverage: 15.2%
  - Total number of restraints: 15
  - Weight of restraints: 1.0 (15)
  - Potential type of restraints: upper-bound-parabolic (15)
  - Range of distance target values: 2.1, 3.1 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map
  - Saveframe: DYANA/DIANA_distance_constraints_5
    - Status: OK
    - Experiment type: noe
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 66, Sequence coverage: 40.9%
    - Total number of restraints: 52
    - Weight of restraints: 1.0 (52)
    - Potential type of restraints: upper-bound-parabolic (52)
    - Range of distance target values: 0.0, 4.0 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
    - Distance restraints on contact map
    - Saveframe: DYANA/DIANA_distance_constraints_7
      - Status: Warning
      - Experiment type: undefined
      - Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 66, Sequence coverage: 15.2%
      - Total number of restraints: 15
        Long range restraints, | i - j | >= 5 : 10
        Total disulfide bond restraints: 5
        S...S (too close!): 2
        Long range: 3
        S...S (too close!): 3
      - Weight of restraints: 1.0 (15)
        Long range restraints, | i - j | >= 5 : 1.0 (10)
        Total disulfide bond restraints: 1.0 (5)
        S...S (too close!): 1.0 (2)
        Long range: 1.0 (3)
        S...S (too close!): 1.0 (3)
      - Potential type of restraints: upper-bound-parabolic (15)
        Long range restraints, | i - j | >= 5 : upper-bound-parabolic (10)
        Total disulfide bond restraints: upper-bound-parabolic (5)
        S...S (too close!): upper-bound-parabolic (2)
        Long range: upper-bound-parabolic (3)
        S...S (too close!): upper-bound-parabolic (3)
      - Range of distance target values: 2.0, 3.0 (Å)
      - Histogram of distance target values
      - Distance restraints per residue
        Chain_ID: A
      - Distance restraints on contact map
      - Saveframe: DYANA/DIANA_distance_constraints_3
        Status: OK
        Experiment type: hbond
        Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 66, Sequence coverage: 39.4%
        Total number of restraints: 40
        Total hydrogen bond restraints: 40
        O...H-x: 3
        O...h-N: 3
        Long range: 34
        O...H-x: 17
        O...h-N: 17
        Weight of restraints: 1.0 (40)
        Total hydrogen bond restraints: 1.0 (40)
        O...H-x: 1.0 (3)
        O...h-N: 1.0 (3)
        Long range: 1.0 (34)
        O...H-x: 1.0 (17)
        O...h-N: 1.0 (17)
        Potential type of restraints: upper-bound-parabolic (40)
        Total hydrogen bond restraints: upper-bound-parabolic (40)
        O...H-x: upper-bound-parabolic (3)
        O...h-N: upper-bound-parabolic (3)
        Long range: upper-bound-parabolic (34)
        O...H-x: upper-bound-parabolic (17)
        O...h-N: upper-bound-parabolic (17)
        Range of distance target values: 2.3, 3.3 (Å)
        Histogram of distance target values
        Distance restraints per residue
        Chain_ID: A
        Distance restraints on contact map
        Saveframe: DYANA/DIANA_distance_constraints_6
        Status: Warning
        Experiment type: hbond
        Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 66, Sequence coverage: 39.4%
        Total number of restraints: 40
        Total hydrogen bond restraints: 40
        O...H-x (too close!): 3
        O...h-N (too close!): 3
        Long range: 34
        O...H-x (too close!): 17
        O...h-N (too close!): 17
        Weight of restraints: 1.0 (40)
        Total hydrogen bond restraints: 1.0 (40)
        O...H-x (too close!): 1.0 (3)
        O...h-N (too close!): 1.0 (3)
        Long range: 1.0 (34)
        O...H-x (too close!): 1.0 (17)
        O...h-N (too close!): 1.0 (17)
        Potential type of restraints: upper-bound-parabolic (40)
        Total hydrogen bond restraints: upper-bound-parabolic (40)
        O...H-x (too close!): upper-bound-parabolic (3)
        O...h-N (too close!): upper-bound-parabolic (3)
        Long range: upper-bound-parabolic (34)
        O...H-x (too close!): upper-bound-parabolic (17)
        O...h-N (too close!): upper-bound-parabolic (17)
        Range of distance target values: 1.8, 2.7 (Å)
        Histogram of distance target values
        Distance restraints per residue
        Chain_ID: A
        Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_8
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 66, Sequence coverage: 98.5%
- Total number of restraints: 158
- Total number of restraints per polymer type: 158
- Weight of restraints: 1.0 (158)
- Potential type of restraints: square-well-parabolic (158)
- Plot of Phi-Psi angle restraints
- Plot of Chi1-Chi2 angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords muscarinic acetylcholine receptors, nicotonic acetylcholine receptors, non-conventional toxin, weak toxin, WTX

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Found 1 Document (0.691 seconds)

BMRB: 19700

Sample #1

Sample #2

Related entities 1. P33A mutant of non-conventional toxin WTX from Naja kaouthia, : 1 : 1 : 111 entities Detail

Experiments performed 6 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 9 contents Detail