BMRBj - BMREntryMaster

Found 1 Document (0.693 seconds)

BMRB: 16260

2KI3

NMR assignments of FK506 binding domain from Plasmodium vivax

Authors

Alag, R., Yoon, H., Shin, J.

Assembly

PvFKBD

Entity

1. PvFKBD (polymer, Thiol state: all free), 126 monomers, 13952.52 Da Detail

MEQETLEQVH LTEDGGVVKT ILRKGEGGEE NAPKKGNEVT VHYVGKLESS GKVFDSSRER NVPFKFHLGQ GEVIKGWDIC VASMTKNEKC SVRLDSKYGY GEEGCGESIP GNSVLIFEIE LISFRE

Formula weight

13952.52 Da

Source organism

Plasmodium vivax

Exptl. method

Refine. method

TORSION ANGLE DYNAMICS

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 99.2 %, Completeness: 92.3 %, Completeness (bb): 96.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	92.3 % (1334 of 1446)	94.7 % (716 of 756)	88.0 % (491 of 558)	96.2 % (127 of 132)
Backbone	96.9 % (727 of 750)	97.4 % (258 of 265)	96.1 % (348 of 362)	98.4 % (121 of 123)
Sidechain	88.6 % (714 of 806)	93.3 % (458 of 491)	81.7 % (250 of 306)	66.7 % (6 of 9)
Aromatic	46.9 % (46 of 98)	93.9 % (46 of 49)	0.0 % (0 of 48)	0.0 % (0 of 1)
Methyl	98.4 % (120 of 122)	96.7 % (59 of 61)	100.0 % (61 of 61)

1. PvFKBD

MEQETLEQVH LTEDGGVVKT ILRKGEGGEE NAPKKGNEVT VHYVGKLESS GKVFDSSRER NVPFKFHLGQ GEVIKGWDIC VASMTKNEKC SVRLDSKYGY GEEGCGESIP GNSVLIFEIE LISFRE

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	PvFKBD	[U-13C; U-15N]		0.5 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	DTT	natural abundance		1 mM
5	sodium azide	natural abundance		0.01 %
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
8	PvFKBD	[U-13C; U-15N]		0.5 mM
9	sodium phosphate	natural abundance		20 mM
10	sodium chloride	natural abundance		50 mM
11	DTT	natural abundance		1 mM
12	sodium azide	natural abundance		0.01 %
13	D2O	natural abundance		100 %

LACS Plot; CA

Referencing offset: -1.19 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: -1.19 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: -0.01 ppm, Outliers: 2 Detail

LACS Plot; CO

Referencing offset: 2.33 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2KI3, Strand ID: A Detail

Release date

2009-10-15

Citation

NMR assignments of the FK506-binding domain of FK506-binding protein 35 from Plasmodium vivax
Alag, R., Shin, J., Yoon, H.
Biomol. NMR Assign. (2009), 3, 243-245, PubMed 19774494 , DOI 10.1007/s12104-009-9185-1 , Abstract

Related entities 1. PvFKBD, : 1 : 6 : 278 entities Detail

Experiments performed 13 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	PvFKBD	[U-13C; U-15N]		0.5 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	DTT	natural abundance		1 mM
5	sodium azide	natural abundance		0.01 %
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

2 3D HNCACB

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	PvFKBD	[U-13C; U-15N]		0.5 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	DTT	natural abundance		1 mM
5	sodium azide	natural abundance		0.01 %
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

3 3D CBCA(CO)NH

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	PvFKBD	[U-13C; U-15N]		0.5 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	DTT	natural abundance		1 mM
5	sodium azide	natural abundance		0.01 %
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

4 3D HNCA

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	PvFKBD	[U-13C; U-15N]		0.5 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	DTT	natural abundance		1 mM
5	sodium azide	natural abundance		0.01 %
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

5 3D HN(CO)CA

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	PvFKBD	[U-13C; U-15N]		0.5 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	DTT	natural abundance		1 mM
5	sodium azide	natural abundance		0.01 %
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

6 3D HNCO

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	PvFKBD	[U-13C; U-15N]		0.5 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	DTT	natural abundance		1 mM
5	sodium azide	natural abundance		0.01 %
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

7 3D HNCACO

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	PvFKBD	[U-13C; U-15N]		0.5 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	DTT	natural abundance		1 mM
5	sodium azide	natural abundance		0.01 %
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

8 3D HNHA

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	PvFKBD	[U-13C; U-15N]		0.5 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	DTT	natural abundance		1 mM
5	sodium azide	natural abundance		0.01 %
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

9 3D H(CCO)NH

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	PvFKBD	[U-13C; U-15N]		0.5 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	DTT	natural abundance		1 mM
5	sodium azide	natural abundance		0.01 %
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

10 3D C(CO)NH

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	PvFKBD	[U-13C; U-15N]		0.5 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	DTT	natural abundance		1 mM
5	sodium azide	natural abundance		0.01 %
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

11 3D 1H-15N NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	PvFKBD	[U-13C; U-15N]		0.5 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	DTT	natural abundance		1 mM
5	sodium azide	natural abundance		0.01 %
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

12 3D HCCH-TOCSY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
8	PvFKBD	[U-13C; U-15N]		0.5 mM
9	sodium phosphate	natural abundance		20 mM
10	sodium chloride	natural abundance		50 mM
11	DTT	natural abundance		1 mM
12	sodium azide	natural abundance		0.01 %
13	D2O	natural abundance		100 %

13 3D 1H-13C NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
8	PvFKBD	[U-13C; U-15N]		0.5 mM
9	sodium phosphate	natural abundance		20 mM
10	sodium chloride	natural abundance		50 mM
11	DTT	natural abundance		1 mM
12	sodium azide	natural abundance		0.01 %
13	D2O	natural abundance		100 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_16260_2ki3.nef
Input source #2: Coordindates	2ki3.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-------100
MEQETLEQVHLTEDGGVVKTILRKGEGGEENAPKKGNEVTVHYVGKLESSGKVFDSSRERNVPFKFHLGQGEVIKGWDICVASMTKNEKCSVRLDSKYGY
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MEQETLEQVHLTEDGGVVKTILRKGEGGEENAPKKGNEVTVHYVGKLESSGKVFDSSRERNVPFKFHLGQGEVIKGWDICVASMTKNEKCSVRLDSKYGY

-------110-------120------
GEEGCGESIPGNSVLIFEIELISFRE
||||||||||||||||||||||||||
GEEGCGESIPGNSVLIFEIELISFRE

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	126	0	0	100.0

Content subtype: combined_16260_2ki3.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1352		99.2 (chain: A, length: 126)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	3651 (1)	noe	99.2 (chain: A, length: 126)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	102 (102)	.	73.8 (chain: A, length: 126)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 126, Sequence coverage: 99.2%
- Total number of assignments
  - ¹H chemical shifts: 728
  - ¹³C chemical shifts: 497
  - ¹⁵N chemical shifts: 127
- 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: 126, Sequence coverage: 99.2%
- Total number of restraints: 3651
- Weight of restraints: 1.0 (3651)
- Potential type of restraints: upper-bound-parabolic (3651)
- Range of distance target values: 2.35, 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_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 126, Sequence coverage: 73.8%
- Total number of restraints: 102
- Total number of restraints per polymer type: 102
- Weight of restraints: 1.0 (102)
- Potential type of restraints: square-well-parabolic (102)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Protein