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BMRB: 19830

2MM8

Structural and biochemical characterization of Jaburetox

Authors

Dobrovolska, O., Lopez, F., Ciurli, S., Zambelli, B., Carlini, C.

Assembly

reduced Jaburetox

Entity

1. reduced Jaburetox (polymer, Thiol state: all free), 93 monomers, 10128.18 Da Detail

MGPVNEANCK AAMEIVCRRE FGHKEEEDAS EGVTTGDPDC PFTKAIPREE YANKYGPTIG DKIRLGDTDL IAEIEKDFAL YGDESVFGGG KVI

Formula weight

10128.18 Da

Source organism

Canavalia ensiformis

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 91.4 %, Completeness: 78.4 %, Completeness (bb): 90.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	78.4 % (806 of 1028)	77.8 % (416 of 535)	76.1 % (306 of 402)	92.3 % (84 of 91)
Backbone	90.3 % (495 of 548)	92.7 % (178 of 192)	86.9 % (233 of 268)	95.5 % (84 of 88)
Sidechain	68.7 % (386 of 562)	69.4 % (238 of 343)	68.5 % (148 of 216)	0.0 % (0 of 3)
Aromatic	2.9 % (2 of 68)	5.9 % (2 of 34)	0.0 % (0 of 34)
Methyl	91.9 % (79 of 86)	95.3 % (41 of 43)	88.4 % (38 of 43)

1. Jbtx

MGPVNEANCK AAMEIVCRRE FGHKEEEDAS EGVTTGDPDC PFTKAIPREE YANKYGPTIG DKIRLGDTDL IAEIEKDFAL YGDESVFGGG KVI

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	Jbtx	[U-99% 13C; U-99% 15N]		1 mM
2	sodium phosphate	natural abundance		50 mM
3	EDTA	natural abundance		1 mM
4	TCEP	natural abundance		1 mM
5	D2O	natural abundance		5 %
6	H2O	natural abundance		95 %

LACS Plot; CA

Referencing offset: 3.01 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: 3.01 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: 0.15 ppm, Outliers: 3 Detail

LACS Plot; CO

Referencing offset: 2.66 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 5 models in PDB: 2MM8, Strand ID: A Detail

Release date

2015-01-19

Citation

1H, 13C, 15N resonance assignments of reduced Jaburetox
Dobrovolska, O., Lopez, F., Zambelli, B., Carlini, C., Ciurli, S.
FEBS

Related entities 1. reduced Jaburetox, : 1 : 20 entities Detail

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	Jbtx	[U-99% 13C; U-99% 15N]		1 mM
2	sodium phosphate	natural abundance		50 mM
3	EDTA	natural abundance		1 mM
4	TCEP	natural abundance		1 mM
5	D2O	natural abundance		5 %
6	H2O	natural abundance		95 %

2 3D HNCO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	Jbtx	[U-99% 13C; U-99% 15N]		1 mM
2	sodium phosphate	natural abundance		50 mM
3	EDTA	natural abundance		1 mM
4	TCEP	natural abundance		1 mM
5	D2O	natural abundance		5 %
6	H2O	natural abundance		95 %

3 3D HNCA

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	Jbtx	[U-99% 13C; U-99% 15N]		1 mM
2	sodium phosphate	natural abundance		50 mM
3	EDTA	natural abundance		1 mM
4	TCEP	natural abundance		1 mM
5	D2O	natural abundance		5 %
6	H2O	natural abundance		95 %

4 3D HN(CO)CA

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	Jbtx	[U-99% 13C; U-99% 15N]		1 mM
2	sodium phosphate	natural abundance		50 mM
3	EDTA	natural abundance		1 mM
4	TCEP	natural abundance		1 mM
5	D2O	natural abundance		5 %
6	H2O	natural abundance		95 %

5 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	Jbtx	[U-99% 13C; U-99% 15N]		1 mM
2	sodium phosphate	natural abundance		50 mM
3	EDTA	natural abundance		1 mM
4	TCEP	natural abundance		1 mM
5	D2O	natural abundance		5 %
6	H2O	natural abundance		95 %

6 3D 1H-13C NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	Jbtx	[U-99% 13C; U-99% 15N]		1 mM
2	sodium phosphate	natural abundance		50 mM
3	EDTA	natural abundance		1 mM
4	TCEP	natural abundance		1 mM
5	D2O	natural abundance		5 %
6	H2O	natural abundance		95 %

7 3D HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	Jbtx	[U-99% 13C; U-99% 15N]		1 mM
2	sodium phosphate	natural abundance		50 mM
3	EDTA	natural abundance		1 mM
4	TCEP	natural abundance		1 mM
5	D2O	natural abundance		5 %
6	H2O	natural abundance		95 %

8 3D CBCA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	Jbtx	[U-99% 13C; U-99% 15N]		1 mM
2	sodium phosphate	natural abundance		50 mM
3	EDTA	natural abundance		1 mM
4	TCEP	natural abundance		1 mM
5	D2O	natural abundance		5 %
6	H2O	natural abundance		95 %

9 3D 1H-15N TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	Jbtx	[U-99% 13C; U-99% 15N]		1 mM
2	sodium phosphate	natural abundance		50 mM
3	EDTA	natural abundance		1 mM
4	TCEP	natural abundance		1 mM
5	D2O	natural abundance		5 %
6	H2O	natural abundance		95 %

10 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	Jbtx	[U-99% 13C; U-99% 15N]		1 mM
2	sodium phosphate	natural abundance		50 mM
3	EDTA	natural abundance		1 mM
4	TCEP	natural abundance		1 mM
5	D2O	natural abundance		5 %
6	H2O	natural abundance		95 %

11 3D HBHA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	Jbtx	[U-99% 13C; U-99% 15N]		1 mM
2	sodium phosphate	natural abundance		50 mM
3	EDTA	natural abundance		1 mM
4	TCEP	natural abundance		1 mM
5	D2O	natural abundance		5 %
6	H2O	natural abundance		95 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_19830_2mm8.nef
Input source #2: Coordindates	2mm8.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	None
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)

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---------
MGPVNEANCKAAMEIVCRREFGHKEEEDASEGVTTGDPDCPFTKAIPREEYANKYGPTIGDKIRLGDTDLIAEIEKDFALYGDESVFGGGKVIHHHHHH
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MGPVNEANCKAAMEIVCRREFGHKEEEDASEGVTTGDPDCPFTKAIPREEYANKYGPTIGDKIRLGDTDLIAEIEKDFALYGDESVFGGGKVIHHHHHH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	99	0	0	100.0

Content subtype: combined_19830_2mm8.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	786		84.8 (chain: A, length: 99)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	1207 (1)	noe	81.8 (chain: A, length: 99)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 99, Sequence coverage: 84.8%
- Total number of assignments
  - ¹H chemical shifts: 405
  - ¹³C chemical shifts: 297
  - ¹⁵N chemical shifts: 84
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 99, Sequence coverage: 81.8%
- Total number of restraints: 1206
- Weight of restraints: 1.0 (1206)
- Potential type of restraints: upper-bound-parabolic (1206)
- Range of distance target values: 1.53, 7.6 (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