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BMRB: 25276

2MVN

Solution structure of eEF1Bdelta CAR domain in TCTP-bound state

Authors

Wu, H., Feng, Y.

Assembly

eEF1Bdelta CAR domain in TCTP-bound state

Entity

1. eEF1Bdelta CAR domain in TCTP-bound state (polymer, Thiol state: not present), 44 monomers, 4992.292 Da Detail

GPGSEDDDID LFGSDNEEED KEAAQLREER LRQYAEKKAK KPAL

Formula weight

4992.292 Da

Source organism

Exptl. method

Refine. method

molecular dynamics simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.7 %, Completeness: 86.9 %, Completeness (bb): 93.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	86.9 % (436 of 502)	85.5 % (230 of 269)	86.2 % (162 of 188)	97.8 % (44 of 45)
Backbone	93.1 % (242 of 260)	91.0 % (81 of 89)	93.0 % (120 of 129)	97.6 % (41 of 42)
Sidechain	81.6 % (231 of 283)	82.8 % (149 of 180)	79.0 % (79 of 100)	100.0 % (3 of 3)
Aromatic	0.0 % (0 of 18)	0.0 % (0 of 9)	0.0 % (0 of 9)
Methyl	86.7 % (26 of 30)	86.7 % (13 of 15)	86.7 % (13 of 15)

1. entity

GPGSEDDDID LFGSDNEEED KEAAQLREER LRQYAEKKAK KPAL

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]		0.2 ~ 0.8 mM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		200 mM
4	DSS	natural abundance		0.01 %
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

LACS Plot; CA

Referencing offset: -0.18 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: -0.18 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: 0.03 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: -0.22 ppm, Outliers: 5 Detail

Protein Blocks Logo

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

Release date

2015-08-24

Citation

Evolutionarily conserved binding of translationally controlled tumor protein to eukaryotic elongation factor 1B
Wu, H., Gong, W., Yao, X., Wang, J., Perrett, S., Feng, Y.
J. Biol. Chem. (2015), 290, 8694-8710, PubMed 25635048 , DOI 10.1074/jbc.M114.628594 , Abstract

Related entities 1. eEF1Bdelta CAR domain in TCTP-bound state, : 1 : 2 : 11 entities Detail

Experiments performed 13 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]		0.2 ~ 0.8 mM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		200 mM
4	DSS	natural abundance		0.01 %
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

2 2D 1H-13C HSQC

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]		0.2 ~ 0.8 mM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		200 mM
4	DSS	natural abundance		0.01 %
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

3 3D CBCA(CO)NH

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]		0.2 ~ 0.8 mM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		200 mM
4	DSS	natural abundance		0.01 %
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

4 3D HNCACB

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]		0.2 ~ 0.8 mM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		200 mM
4	DSS	natural abundance		0.01 %
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

5 3D HNCO

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]		0.2 ~ 0.8 mM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		200 mM
4	DSS	natural abundance		0.01 %
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

6 3D HN(CA)CO

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]		0.2 ~ 0.8 mM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		200 mM
4	DSS	natural abundance		0.01 %
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

7 3D HBHA(CO)NH

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]		0.2 ~ 0.8 mM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		200 mM
4	DSS	natural abundance		0.01 %
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

8 3D HBHANH

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]		0.2 ~ 0.8 mM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		200 mM
4	DSS	natural abundance		0.01 %
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

9 3D HCCH-TOCSY

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]		0.2 ~ 0.8 mM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		200 mM
4	DSS	natural abundance		0.01 %
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

10 3D CCH-TOCSY

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]		0.2 ~ 0.8 mM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		200 mM
4	DSS	natural abundance		0.01 %
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

11 3D CCH-COSY

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]		0.2 ~ 0.8 mM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		200 mM
4	DSS	natural abundance		0.01 %
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

12 3D 1H-15N NOESY

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]		0.2 ~ 0.8 mM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		200 mM
4	DSS	natural abundance		0.01 %
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

13 3D 1H-13C NOESY

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]		0.2 ~ 0.8 mM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		200 mM
4	DSS	natural abundance		0.01 %
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25276_2mvn.nef
Input source #2: Coordindates	2mvn.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

-150-----160-------170-------180-------190--
GPGSEDDDIDLFGSDNEEEDKEAAQLREERLRQYAEKKAKKPAL
||||||||||||||||||||||||||||||||||||||||||||
GPGSEDDDIDLFGSDNEEEDKEAAQLREERLRQYAEKKAKKPAL
--------10--------20--------30--------40----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	44	0	0	100.0

Content subtype: combined_25276_2mvn.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	433		97.7 (chain: A, length: 44)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	571 (1)	noe	97.7 (chain: A, length: 44)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	30 (1)	hbond	43.2 (chain: A, length: 44)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	55 (55)	.	79.5 (chain: A, length: 44)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 44, Sequence coverage: 97.7%
- Total number of assignments
  - ¹H chemical shifts: 230
  - ¹³C chemical shifts: 159
  - ¹⁵N chemical shifts: 44
- Completeness of assignments
  - Entity_assemble_ID: A
- 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: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 44, Sequence coverage: 97.7%
- Total number of restraints: 569
- Weight of restraints: 1.0 (569)
- Potential type of restraints: square-well-parabolic (569)
- Range of distance target values: 2.09, 3.91 (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
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 44, Sequence coverage: 43.2%
  - Total number of restraints: 30
  - Weight of restraints: 1.0 (30)
  - Potential type of restraints: square-well-parabolic (30)
  - 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

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 44, Sequence coverage: 79.5%
- Total number of restraints: 55
- Total number of restraints per polymer type: 55
- Weight of restraints: 1.0 (55)
- Potential type of restraints: square-well-parabolic (55)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords GUANINE NUCLEOTIDE EXCHANGE FACTOR