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BMRB: 19535

2MF3

SGTX-Sf1a

Authors

Mobli, M., Bende, N.S., King, G.F.

Assembly

SGTX-Sf1a

Entity

1. SGTX-Sf1a (polymer, Thiol state: all disulfide bound), 47 monomers, 5068.877 Da Detail

SKECMTDGTV CYIHNHNDCC GSCLCSNGPI ARPWEMMVGN CMCGPKA

Formula weight

5068.877 Da

Entity Connection

disulfide 4 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS4:SG	1:CYS20:SG
2	disulfide	sing	1:CYS11:SG	1:CYS23:SG
3	disulfide	sing	1:CYS19:SG	1:CYS43:SG
4	disulfide	sing	1:CYS25:SG	1:CYS41:SG

Source organism

Segestria florentina

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 96.8 %, Completeness (bb): 97.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	96.8 % (477 of 493)	96.5 % (247 of 256)	96.8 % (182 of 188)	98.0 % (48 of 49)
Backbone	97.1 % (268 of 276)	96.9 % (93 of 96)	97.1 % (132 of 136)	97.7 % (43 of 44)
Sidechain	96.9 % (251 of 259)	96.2 % (154 of 160)	97.9 % (92 of 94)	100.0 % (5 of 5)
Aromatic	92.9 % (26 of 28)	100.0 % (14 of 14)	84.6 % (11 of 13)	100.0 % (1 of 1)
Methyl	100.0 % (28 of 28)	100.0 % (14 of 14)	100.0 % (14 of 14)

1. SF1A

SKECMTDGTV CYIHNHNDCC GSCLCSNGPI ARPWEMMVGN CMCGPKA

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 3.5

#	Name	Isotope labeling	Type	Concentration
1	SF1A	[U-99% 13C; U-99% 15N]		0.42 mM
2	D2O	[U-100% 2H]		5 %
3	Sodium citrate	natural abundance		20 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

LACS Plot; CA

Referencing offset: -0.31 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: -0.31 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: -0.16 ppm, Outliers: 2 Detail

LACS Plot; CO

Referencing offset: 1.13 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2MF3, Strand ID: A Detail

Release date

2014-10-12

Citation

Structure of SGTX1-SF1A
Mobli, M., Bende, N.S., King, G.F., Volker, H.
Not known

Related entities 1. SGTX-Sf1a, : 1 : 3 : 5 entities Detail

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 3.5

#	Name	Isotope labeling	Type	Concentration
1	SF1A	[U-99% 13C; U-99% 15N]		0.42 mM
2	D2O	[U-100% 2H]		5 %
3	Sodium citrate	natural abundance		20 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

2 3D CBCA(CO)NH

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 3.5

#	Name	Isotope labeling	Type	Concentration
1	SF1A	[U-99% 13C; U-99% 15N]		0.42 mM
2	D2O	[U-100% 2H]		5 %
3	Sodium citrate	natural abundance		20 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

3 3D HBHA(CO)NH

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 3.5

#	Name	Isotope labeling	Type	Concentration
1	SF1A	[U-99% 13C; U-99% 15N]		0.42 mM
2	D2O	[U-100% 2H]		5 %
3	Sodium citrate	natural abundance		20 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

4 3D HNCACB

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 3.5

#	Name	Isotope labeling	Type	Concentration
1	SF1A	[U-99% 13C; U-99% 15N]		0.42 mM
2	D2O	[U-100% 2H]		5 %
3	Sodium citrate	natural abundance		20 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

5 3D 1H-15N NOESY

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 3.5

#	Name	Isotope labeling	Type	Concentration
1	SF1A	[U-99% 13C; U-99% 15N]		0.42 mM
2	D2O	[U-100% 2H]		5 %
3	Sodium citrate	natural abundance		20 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

6 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 3.5

#	Name	Isotope labeling	Type	Concentration
1	SF1A	[U-99% 13C; U-99% 15N]		0.42 mM
2	D2O	[U-100% 2H]		5 %
3	Sodium citrate	natural abundance		20 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

7 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 3.5

#	Name	Isotope labeling	Type	Concentration
1	SF1A	[U-99% 13C; U-99% 15N]		0.42 mM
2	D2O	[U-100% 2H]		5 %
3	Sodium citrate	natural abundance		20 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

8 4D HC(CO)NH

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 3.5

#	Name	Isotope labeling	Type	Concentration
1	SF1A	[U-99% 13C; U-99% 15N]		0.42 mM
2	D2O	[U-100% 2H]		5 %
3	Sodium citrate	natural abundance		20 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

9 2D (HB)CB(CGCC)H(ar)

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 3.5

#	Name	Isotope labeling	Type	Concentration
1	SF1A	[U-99% 13C; U-99% 15N]		0.42 mM
2	D2O	[U-100% 2H]		5 %
3	Sodium citrate	natural abundance		20 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

10 3D HNCO

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 3.5

#	Name	Isotope labeling	Type	Concentration
1	SF1A	[U-99% 13C; U-99% 15N]		0.42 mM
2	D2O	[U-100% 2H]		5 %
3	Sodium citrate	natural abundance		20 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_19535_2mf3.nef
Input source #2: Coordindates	2mf3.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:4:CYS:SG	A:20:CYS:SG	oxidized, CA 54.15, CB 42.39 ppm	oxidized, CA 57.344, CB 39.211 ppm	2.121
A:11:CYS:SG	A:23:CYS:SG	oxidized, CA 53.788, CB 49.168 ppm	oxidized, CA 55.865, CB 39.214 ppm	1.98
A:19:CYS:SG	A:43:CYS:SG	oxidized, CA 55.126, CB 36.169 ppm	oxidized, CA 53.494, CB 35.707 ppm	2.123
A:25:CYS:SG	A:41:CYS:SG	oxidized, CA 54.567, CB 45.295 ppm	oxidized, CA 56.317, CB 48.409 ppm	2.12

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-------
SKECMTDGTVCYIHNHNDCCGSCLCSNGPIARPWEMMVGNCMCGPKA
|||||||||||||||||||||||||||||||||||||||||||||||
SKECMTDGTVCYIHNHNDCCGSCLCSNGPIARPWEMMVGNCMCGPKA

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	47	0	0	100.0

Content subtype: combined_19535_2mf3.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	4		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	486		100.0 (chain: A, length: 47)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	717 (1)	noe	100.0 (chain: A, length: 47)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 47, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 255
  - ¹³C chemical shifts: 182
  - ¹⁵N chemical shifts: 49
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Tautomeric state of HIS
- 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

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: 47, Sequence coverage: 100.0%
- Total number of restraints: 712
- Weight of restraints: 1.0 (712)
- Potential type of restraints: upper-bound-parabolic (712)
- Range of distance target values: 2.8, 5.5 (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

Keywords Disulfide, Heteronuclear, ICK, Insecticidal, Maximum entropy, Non-uniform sampling, Spider, Toxin