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BMRB: 18954

2M3D

NMR structure of the GUCT domain from human DEAD box polypeptide 21

Authors

Dutta, S.K., Serrano, P., Geralt, M., Wuthrich, K.

Assembly

GUCT

Entity

1. GUCT (polymer, Thiol state: all free), 95 monomers, 10628.04 Da Detail

GHISGATSVD QRSLINSNVG FVTMILQCSI EMPNISYAWK ELKEQLGEEI DSKVKGMVFL KGKLGVCFDV PTASVTEIQE KWHDSRRWQL SVATE

Formula weight

10628.04 Da

Source organism

Exptl. method

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.9 %, Completeness: 87.4 %, Completeness (bb): 83.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	87.4 % (970 of 1110)	94.8 % (545 of 575)	74.9 % (323 of 431)	98.1 % (102 of 104)
Backbone	83.0 % (470 of 566)	96.4 % (188 of 195)	68.7 % (191 of 278)	97.8 % (91 of 93)
Sidechain	92.9 % (587 of 632)	93.9 % (357 of 380)	90.9 % (219 of 241)	100.0 % (11 of 11)
Aromatic	76.8 % (63 of 82)	85.4 % (35 of 41)	65.8 % (25 of 38)	100.0 % (3 of 3)
Methyl	93.6 % (103 of 110)	96.4 % (53 of 55)	90.9 % (50 of 55)

1. entity

GHISGATSVD QRSLINSNVG FVTMILQCSI EMPNISYAWK ELKEQLGEEI DSKVKGMVFL KGKLGVCFDV PTASVTEIQE KWHDSRRWQL SVATE

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	GUCT	[U-99% 13C; U-99% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		5 mM
5	D2O	[U-99% 2H]		95 %
6	H2O	natural abundance		5 %

LACS Plot; CA

Referencing offset: 2.3 ppm, Outliers: 3 Detail

LACS Plot; CB

Referencing offset: 2.3 ppm, Outliers: 3 Detail

LACS Plot; HA

Referencing offset: 0.07 ppm, Outliers: 5 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2M3D, Strand ID: A Detail

Release date

2013-01-27

Citation

NMR structure of the GUCT domain from human DEAD box polypeptide 21 (DDX21)
Dutta, S.K., Serrano, P., Geralt, M., Wuthrich, K.
Not known

Related entities 1. GUCT, : 1 : 2 : 16 entities Detail

Interaction partners 1. GUCT, : 113 interactors Detail

More details for 113 interactors identified by 39 citations

Experiments performed 7 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 6.0

#	Name	Isotope labeling	Type	Concentration
1	GUCT	[U-99% 13C; U-99% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		5 mM
5	D2O	[U-99% 2H]		95 %
6	H2O	natural abundance		5 %

2 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	GUCT	[U-99% 13C; U-99% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		5 mM
5	D2O	[U-99% 2H]		95 %
6	H2O	natural abundance		5 %

3 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	GUCT	[U-99% 13C; U-99% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		5 mM
5	D2O	[U-99% 2H]		95 %
6	H2O	natural abundance		5 %

4 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 6.0

#	Name	Isotope labeling	Type	Concentration
1	GUCT	[U-99% 13C; U-99% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		5 mM
5	D2O	[U-99% 2H]		95 %
6	H2O	natural abundance		5 %

5 4D APSY HACANH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	GUCT	[U-99% 13C; U-99% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		5 mM
5	D2O	[U-99% 2H]		95 %
6	H2O	natural abundance		5 %

6 5D APSY HACACONH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	GUCT	[U-99% 13C; U-99% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		5 mM
5	D2O	[U-99% 2H]		95 %
6	H2O	natural abundance		5 %

7 5D APSY CBCACONH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	GUCT	[U-99% 13C; U-99% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		5 mM
5	D2O	[U-99% 2H]		95 %
6	H2O	natural abundance		5 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_18954_2m3d.nef
Input source #2: Coordindates	2m3d.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-----
GHISGATSVDQRSLINSNVGFVTMILQCSIEMPNISYAWKELKEQLGEEIDSKVKGMVFLKGKLGVCFDVPTASVTEIQEKWHDSRRWQLSVATE
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GHISGATSVDQRSLINSNVGFVTMILQCSIEMPNISYAWKELKEQLGEEIDSKVKGMVFLKGKLGVCFDVPTASVTEIQEKWHDSRRWQLSVATE

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	95	0	0	100.0

Content subtype: combined_18954_2m3d.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	954		97.9 (chain: A, length: 95)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	1798 (1)	noe	97.9 (chain: A, length: 95)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 95, Sequence coverage: 97.9%
- Total number of assignments
  - ¹H chemical shifts: 546
  - ¹³C chemical shifts: 307
  - ¹⁵N chemical shifts: 101
- 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

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 95, Sequence coverage: 97.9%
- Total number of restraints: 1785
- Weight of restraints: 1.0 (1785)
- Potential type of restraints: upper-bound-parabolic (1785)
- Range of distance target values: 2.4, 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 DEAD box polypeptide 21, GUCT domain, RNA helicase II/Gu, RRM fold