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BMRB: 25970

2NBB

NMR structure of the Acidic domain of SYNCRIP (24-140)

Authors

Serrano, P., Wuthrich, K., Beuck, C.

Assembly

Acidic domain of SYNCRIP (24-140)

Entity

1. Acidic domain of SYNCRIP (24-140) (polymer), 118 monomers, 12915.33 Da Detail

GSENFQTLLD AGLPQKVAEK LDEIYVAGLV AHSDLDERAI EALKEFNEDG ALAVLQQFKD SDLSHVQNKS AFLCGVMKTY RQREKQGTKV ADSSKGPDEA KIKALLERTG YTLDVTTG

Formula weight

12915.33 Da

Source organism

Exptl. method

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 92.9 %, Completeness (bb): 96.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	92.9 % (1245 of 1340)	91.9 % (639 of 695)	92.5 % (480 of 519)	100.0 % (126 of 126)
Backbone	96.0 % (676 of 704)	97.1 % (236 of 243)	93.9 % (324 of 345)	100.0 % (116 of 116)
Sidechain	90.9 % (677 of 745)	89.2 % (403 of 452)	93.3 % (264 of 283)	100.0 % (10 of 10)
Aromatic	80.6 % (58 of 72)	83.3 % (30 of 36)	77.8 % (28 of 36)
Methyl	97.1 % (134 of 138)	95.7 % (66 of 69)	98.6 % (68 of 69)

1. entity

GSENFQTLLD AGLPQKVAEK LDEIYVAGLV AHSDLDERAI EALKEFNEDG ALAVLQQFKD SDLSHVQNKS AFLCGVMKTY RQREKQGTKV ADSSKGPDEA KIKALLERTG YTLDVTTG

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	entity	[U-99% 13C; U-98% 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

LACS Plot; CA

Referencing offset: 2.73 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: 2.73 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: 0.13 ppm, Outliers: 3 Detail

LACS Plot; CO

Referencing offset: 2.63 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 19 models in PDB: 2NBB, Strand ID: A Detail

Release date

2016-05-30

Citation

The acidic domain is a unique structural feature of the splicing factor SYNCRIP
Beuck, C., Williamson, J.R., Wuthrich, K., Serrano, P.
Protein Sci. (2016), 25, 1545-1550, PubMed 27081926 , DOI 10.1002/pro.2935 , Abstract

Related entities 1. Acidic domain of SYNCRIP (24-140), : 1 : 4 : 14 entities Detail

Interaction partners 1. Acidic domain of SYNCRIP (24-140), : 16 interactors Detail

More details for 16 interactors identified by 2 citations

Experiments performed 7 experiments Detail

1 APSY 4D-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	entity	[U-99% 13C; U-98% 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

2 APSY 5D-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	entity	[U-99% 13C; U-98% 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

3 APSY 5D-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	entity	[U-99% 13C; U-98% 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

4 2D 1H-15N HSQC

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	entity	[U-99% 13C; U-98% 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 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	entity	[U-99% 13C; U-98% 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

6 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	entity	[U-99% 13C; U-98% 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

7 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	entity	[U-99% 13C; U-98% 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

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_25970_2nbb.nef
Input source #2: Coordindates	2nbb.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
GSENFQTLLDAGLPQKVAEKLDEIYVAGLVAHSDLDERAIEALKEFNEDGALAVLQQFKDSDLSHVQNKSAFLCGVMKTYRQREKQGTKVADSSKGPDEA
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSENFQTLLDAGLPQKVAEKLDEIYVAGLVAHSDLDERAIEALKEFNEDGALAVLQQFKDSDLSHVQNKSAFLCGVMKTYRQREKQGTKVADSSKGPDEA

-------110--------
KIKALLERTGYTLDVTTG
||||||||||||||||||
KIKALLERTGYTLDVTTG

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	118	0	0	100.0

Content subtype: combined_25970_2nbb.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1248		100.0 (chain: A, length: 118)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	1867 (1)	noe	99.2 (chain: A, length: 118)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 118, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 643
  - ¹³C chemical shifts: 478
  - ¹⁵N chemical shifts: 127
- 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: 118, Sequence coverage: 99.2%
- Total number of restraints: 1867
- Weight of restraints: 1.0 (1867)
- Potential type of restraints: upper-bound-parabolic (1867)
- 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 Acidic domain, SYNCRIP