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BMRB: 19027

2M4Y

Backbone 1H, 13C, and 15N Chemical Shift Assignments for rubredoxin type protein from Mycobacterium ulcerans

Authors

Barnwal, R., Varani, G.

Assembly

rubredoxin type protein from Mycobacterium ulcerans

Entity

1. rubredoxin type protein from Mycobacterium ulcerans (polymer, Thiol state: all free), 56 monomers, 6454.116 Da Detail

MTAYRCPVCD YTYDEGKGDP REGFPAGTRW DQIPDDWCCP DCSVREKVDF ERMGGK

Formula weight

6454.116 Da

Source organism

Mycobacterium ulcerans

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 83.7 %, Completeness (bb): 96.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	83.7 % (527 of 630)	81.6 % (271 of 332)	84.0 % (205 of 244)	94.4 % (51 of 54)
Backbone	96.6 % (315 of 326)	96.5 % (109 of 113)	96.3 % (156 of 162)	98.0 % (50 of 51)
Sidechain	74.0 % (262 of 354)	74.0 % (162 of 219)	75.0 % (99 of 132)	33.3 % (1 of 3)
Aromatic	30.9 % (21 of 68)	50.0 % (17 of 34)	12.5 % (4 of 32)	0.0 % (0 of 2)
Methyl	84.6 % (22 of 26)	84.6 % (11 of 13)	84.6 % (11 of 13)

1. rubredoxin type protein

MTAYRCPVCD YTYDEGKGDP REGFPAGTRW DQIPDDWCCP DCSVREKVDF ERMGGK

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	rubredoxin type protein	[U-98% 15N]		1.2 mM
2	rubredoxin type protein	[U-95% 13C; U-95% 15N]		1.4 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

LACS Plot; CA

Referencing offset: -1.46 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: -1.46 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: 0.16 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: 0.1 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 2M4Y, Strand ID: A Detail

Release date

2013-03-11

Related entities 1. rubredoxin type protein from Mycobacterium ulcerans, : 1 : 112 entities Detail

Experiments performed 8 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AMX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	rubredoxin type protein	[U-98% 15N]		1.2 mM
2	rubredoxin type protein	[U-95% 13C; U-95% 15N]		1.4 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

2 2D 1H-13C HSQC

Instrument

Bruker AMX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	rubredoxin type protein	[U-98% 15N]		1.2 mM
2	rubredoxin type protein	[U-95% 13C; U-95% 15N]		1.4 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

3 3D CBCA(CO)NH

Instrument

Bruker AMX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	rubredoxin type protein	[U-98% 15N]		1.2 mM
2	rubredoxin type protein	[U-95% 13C; U-95% 15N]		1.4 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

4 3D HNCO

Instrument

Bruker AMX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	rubredoxin type protein	[U-98% 15N]		1.2 mM
2	rubredoxin type protein	[U-95% 13C; U-95% 15N]		1.4 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

5 3D HNCACB

Instrument

Bruker AMX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	rubredoxin type protein	[U-98% 15N]		1.2 mM
2	rubredoxin type protein	[U-95% 13C; U-95% 15N]		1.4 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

6 3D HCCH-TOCSY

Instrument

Bruker AMX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	rubredoxin type protein	[U-98% 15N]		1.2 mM
2	rubredoxin type protein	[U-95% 13C; U-95% 15N]		1.4 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

7 3D 1H-15N NOESY

Instrument

Bruker AMX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	rubredoxin type protein	[U-98% 15N]		1.2 mM
2	rubredoxin type protein	[U-95% 13C; U-95% 15N]		1.4 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

8 3D 1H-13C NOESY

Instrument

Bruker AMX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	rubredoxin type protein	[U-98% 15N]		1.2 mM
2	rubredoxin type protein	[U-95% 13C; U-95% 15N]		1.4 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19027_2m4y.nef
Input source #2: Coordindates	2m4y.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------
MTAYRCPVCDYTYDEGKGDPREGFPAGTRWDQIPDDWCCPDCSVREKVDFERMGGK
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MTAYRCPVCDYTYDEGKGDPREGFPAGTRWDQIPDDWCCPDCSVREKVDFERMGGK

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	56	0	0	100.0

Content subtype: combined_19027_2m4y.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	519		100.0 (chain: A, length: 56)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	652 (1)	noe	100.0 (chain: A, length: 56)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_4	OK	88 (88)	.	92.9 (chain: A, length: 56)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 56, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 262
  - ¹³C chemical shifts: 206
  - ¹⁵N chemical shifts: 51
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- 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: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 56, Sequence coverage: 100.0%
- Total number of restraints: 650
- Weight of restraints: 1.0 (650)
- Potential type of restraints: upper-bound-parabolic (650)
- Range of distance target values: 2.23, 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

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 56, Sequence coverage: 92.9%
- Total number of restraints: 88
- Total number of restraints per polymer type: 88
- Weight of restraints: 1.0 (88)
- Potential type of restraints: square-well-parabolic (88)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords NMR, rubredoxin