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BMRB: 15695

2K28

Solution NMR structure of the chromobox protein homolog 4

Authors

Kaustov, L., Lemak, A., Quyang, H., Fares, C., Gutmanas, A., Ravichandran, M., Loppnau, P., Bountra, C., Weigelt, J., Edwards, A., Min, J., Arrowsmith, C.

Assembly

chromobox protein homolog 4

Entity

1. chromobox protein homolog 4 (polymer, Thiol state: all free), 60 monomers, 7341.219 Da Detail

GSEHVFAVES IEKKRIRKGR VEYLVKWRGW SPKYNTWEPE ENILDPRLLI AFQNRERQEQ

Formula weight

7341.219 Da

Source organism

Exptl. method

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 98.3 %, Completeness: 87.5 %, Completeness (bb): 90.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	87.5 % (673 of 769)	86.6 % (356 of 411)	88.7 % (259 of 292)	87.9 % (58 of 66)
Backbone	90.1 % (319 of 354)	89.2 % (107 of 120)	90.4 % (160 of 177)	91.2 % (52 of 57)
Sidechain	86.7 % (409 of 472)	85.6 % (249 of 291)	89.5 % (154 of 172)	66.7 % (6 of 9)
Aromatic	73.7 % (56 of 76)	84.2 % (32 of 38)	62.9 % (22 of 35)	66.7 % (2 of 3)
Methyl	92.6 % (50 of 54)	85.2 % (23 of 27)	100.0 % (27 of 27)

1. cbx4

GSEHVFAVES IEKKRIRKGR VEYLVKWRGW SPKYNTWEPE ENILDPRLLI AFQNRERQEQ

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	phosphate	natural abundance		0.5 mM
2	phosphate	natural abundance		10 mM
3	sodium chloride	natural abundance		300 mM
4	DTT	natural abundance		2 mM

LACS Plot; CA

Referencing offset: 0.51 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: 0.51 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: 0.05 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: 0.07 ppm, Outliers: 3 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2K28, Strand ID: A Detail

Release date

2008-03-27

Citation

Solution NMR structure of the chromobox protein homolog 4
Kaustov, L., Lemak, A., Quyang, H., Fares, C., Gutmanas, A., Ravichandran, M., Loppnau, P., Bountra, C., Weigelt, J., Edwards, A., Min, J., Arrowsmith, C.

Related entities 1. chromobox protein homolog 4, : 1 : 1 : 6 : 165 entities Detail

Interaction partners 1. chromobox protein homolog 4, : 3 interactors Detail

More details for 3 interactors identified by 3 citations

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	phosphate	natural abundance		0.5 mM
2	phosphate	natural abundance		10 mM
3	sodium chloride	natural abundance		300 mM
4	DTT	natural abundance		2 mM

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	phosphate	natural abundance		0.5 mM
2	phosphate	natural abundance		10 mM
3	sodium chloride	natural abundance		300 mM
4	DTT	natural abundance		2 mM

3 3D HNCO

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	phosphate	natural abundance		0.5 mM
2	phosphate	natural abundance		10 mM
3	sodium chloride	natural abundance		300 mM
4	DTT	natural abundance		2 mM

4 3D HBHA(CO)NH

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	phosphate	natural abundance		0.5 mM
2	phosphate	natural abundance		10 mM
3	sodium chloride	natural abundance		300 mM
4	DTT	natural abundance		2 mM

5 3D CBCA(CO)NH

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	phosphate	natural abundance		0.5 mM
2	phosphate	natural abundance		10 mM
3	sodium chloride	natural abundance		300 mM
4	DTT	natural abundance		2 mM

6 3D HNCA

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	phosphate	natural abundance		0.5 mM
2	phosphate	natural abundance		10 mM
3	sodium chloride	natural abundance		300 mM
4	DTT	natural abundance		2 mM

7 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	phosphate	natural abundance		0.5 mM
2	phosphate	natural abundance		10 mM
3	sodium chloride	natural abundance		300 mM
4	DTT	natural abundance		2 mM

8 3D (H)CCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	phosphate	natural abundance		0.5 mM
2	phosphate	natural abundance		10 mM
3	sodium chloride	natural abundance		300 mM
4	DTT	natural abundance		2 mM

9 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	phosphate	natural abundance		0.5 mM
2	phosphate	natural abundance		10 mM
3	sodium chloride	natural abundance		300 mM
4	DTT	natural abundance		2 mM

10 3D 1H-13C NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	phosphate	natural abundance		0.5 mM
2	phosphate	natural abundance		10 mM
3	sodium chloride	natural abundance		300 mM
4	DTT	natural abundance		2 mM

11 3D aromat 1H-13C NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	phosphate	natural abundance		0.5 mM
2	phosphate	natural abundance		10 mM
3	sodium chloride	natural abundance		300 mM
4	DTT	natural abundance		2 mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15695_2k28.nef
Input source #2: Coordindates	2k28.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
GSEHVFAVESIEKKRIRKGRVEYLVKWRGWSPKYNTWEPEENILDPRLLIAFQNRERQEQ
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSEHVFAVESIEKKRIRKGRVEYLVKWRGWSPKYNTWEPEENILDPRLLIAFQNRERQEQ

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	60	0	0	100.0

Content subtype: combined_15695_2k28.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	693		98.3 (chain: A, length: 60)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	1639 (1)	noe	95.0 (chain: A, length: 60)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	74 (74)	.	81.7 (chain: A, length: 60)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 60, Sequence coverage: 98.3%
- Total number of assignments
  - ¹H chemical shifts: 375
  - ¹³C chemical shifts: 262
  - ¹⁵N chemical shifts: 56
- Completeness of assignments
  - Entity_assemble_ID: A
- 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: CNS/XPLOR_distance_constraints_3
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 60, Sequence coverage: 95.0%
- Total number of restraints: 1639
- Weight of restraints: 1.0 (1639)
- Potential type of restraints: square-well-parabolic (1639)
- Range of distance target values: 2.25, 3.9 (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: CNS/XPLOR_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 60, Sequence coverage: 81.7%
- Total number of restraints: 74
- Total number of restraints per polymer type: 74
- Weight of restraints: 1.0 (74)
- Potential type of restraints: square-well-parabolic (74)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords alpha/beta protein