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BMRB: 25837

2N88

Chemical shift assignment, NMR constraints and PDB for chromodomain 3 (CD3) of cpSRP43

Authors

Hennig, J., Sattler, M.

Assembly

chromodomain 3 (CD3) of cpSRP43

Entity

1. chromodomain 3 (CD3) of cpSRP43 (polymer, Thiol state: not present), 58 monomers, 6576.198 Da Detail

GLEYAVAESV IGKRVGDDGK TIEYLVKWTD MSDATWEPQD NVDSTLVLLY QQQQPMNE

Formula weight

6576.198 Da

Source organism

Arabidopsis thaliana

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 97.8 %, Completeness (bb): 99.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	97.8 % (653 of 668)	98.8 % (341 of 345)	95.7 % (247 of 258)	100.0 % (65 of 65)
Backbone	99.7 % (343 of 344)	99.2 % (117 of 118)	100.0 % (170 of 170)	100.0 % (56 of 56)
Sidechain	96.3 % (364 of 378)	98.7 % (224 of 227)	92.3 % (131 of 142)	100.0 % (9 of 9)
Aromatic	87.5 % (42 of 48)	100.0 % (24 of 24)	72.7 % (16 of 22)	100.0 % (2 of 2)
Methyl	97.0 % (64 of 66)	100.0 % (33 of 33)	93.9 % (31 of 33)

1. CD3

GLEYAVAESV IGKRVGDDGK TIEYLVKWTD MSDATWEPQD NVDSTLVLLY QQQQPMNE

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	CD3	[U-100% 13C; U-100% 15N]		0.26 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
2	CD3	[U-100% 13C; U-100% 15N]		0.8 mM

LACS Plot; CA

Referencing offset: 0.19 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: 0.19 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: -0.03 ppm, Outliers: 3 Detail

LACS Plot; CO

Referencing offset: 0.45 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 9 models in PDB: 2N88, Strand ID: A Detail

Release date

2015-12-06

Citation

Structural basis for cpSRP43 chromodomain selectivity and dynamics in Alb3 insertase interaction
Horn, A., Hennig, J., Ahmed, Y.L., Stier, G., Wild, K., Sattler, M., Sinning, I.
Nat. Commun. (2015), 6, 8875-8875, PubMed 26568381 , DOI 10.1038/ncomms9875 , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 25838 released on 2016-01-05
Title Backbone 1H, 13C, and 15N Chemical Shift Assignments for the C-terminal intrinsically disordered domain of Alb3

Related entities 1. chromodomain 3 (CD3) of cpSRP43, : 1 : 2 : 3 : 50 entities Detail

Interaction partners 1. chromodomain 3 (CD3) of cpSRP43, : 21 interactors Detail

More details for 21 interactors identified by 5 citations

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance III - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	CD3	[U-100% 13C; U-100% 15N]		0.26 mM

2 3D HNCA

Instrument

Bruker Avance III - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	CD3	[U-100% 13C; U-100% 15N]		0.26 mM

3 3D HNCACB

Instrument

Bruker Avance III - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	CD3	[U-100% 13C; U-100% 15N]		0.26 mM

4 3D HNCO

Instrument

Bruker Avance III - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	CD3	[U-100% 13C; U-100% 15N]		0.26 mM

5 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance III - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	CD3	[U-100% 13C; U-100% 15N]		0.26 mM

6 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance III - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	CD3	[U-100% 13C; U-100% 15N]		0.26 mM

7 3D HCCH-TOCSY

Instrument

Bruker Avance III - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	CD3	[U-100% 13C; U-100% 15N]		0.26 mM

8 3D HCCH-TOCSY

Instrument

Bruker Avance III - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	CD3	[U-100% 13C; U-100% 15N]		0.26 mM

9 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance III - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
2	CD3	[U-100% 13C; U-100% 15N]		0.8 mM

10 3D 1H-15N NOESY

Instrument

Bruker Avance III - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
2	CD3	[U-100% 13C; U-100% 15N]		0.8 mM

11 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance III - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
2	CD3	[U-100% 13C; U-100% 15N]		0.8 mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25837_2n88.nef
Input source #2: Coordindates	2n88.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

-50-------60--------70--------80--------90-------100------
GLEYAVAESVIGKRVGDDGKTIEYLVKWTDMSDATWEPQDNVDSTLVLLYQQQQPMNE
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GLEYAVAESVIGKRVGDDGKTIEYLVKWTDMSDATWEPQDNVDSTLVLLYQQQQPMNE
--------10--------20--------30--------40--------50--------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	58	0	0	100.0

Content subtype: combined_25837_2n88.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	651		100.0 (chain: A, length: 58)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	1035 (1)	noe	94.8 (chain: A, length: 58)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	534 (534)	.	100.0 (chain: A, length: 58)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 58, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 342
  - ¹³C chemical shifts: 242
  - ¹⁵N chemical shifts: 67
- 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: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 58, Sequence coverage: 94.8%
- Total number of restraints: 1035
- Weight of restraints: 1.0 (1035)
- Potential type of restraints: upper-bound-parabolic (1035)
- Range of distance target values: 2.8, 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: 58, Sequence coverage: 100.0%
- Total number of restraints: 534
- Total number of restraints per polymer type: 534
- Weight of restraints: 1.0 (534)
- Potential type of restraints: square-well-parabolic (534)
- Plot of Phi-Psi angle restraints
- Plot of Chi1-Chi2 angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords SRP, chromodomain, cpSRP, membrane trafficking, plant signaling