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BMRB: 15674

2K1B

Solution NMR structure of the chromobox protein homolog 7

Authors

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

Assembly

chromobox protein homolog 7

Entity

1. chromobox protein homolog 7 (polymer, Thiol state: all free), 73 monomers, 8940.018 Da Detail

MHHHHHHSSG RENLYFQGEQ VFAVESIRKK RVRKGKVEYL VKWKGWPPKY STWEPEEHIL DPRLVMAYEE KEE

Formula weight

8940.018 Da

Source organism

Exptl. method

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 76.7 %, Completeness: 71.1 %, Completeness (bb): 71.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	71.1 % (658 of 926)	72.3 % (355 of 491)	69.7 % (251 of 360)	69.3 % (52 of 75)
Backbone	71.6 % (308 of 430)	71.2 % (104 of 146)	72.1 % (155 of 215)	71.0 % (49 of 69)
Sidechain	71.5 % (404 of 565)	72.8 % (251 of 345)	70.1 % (150 of 214)	50.0 % (3 of 6)
Aromatic	36.2 % (42 of 116)	43.1 % (25 of 58)	27.3 % (15 of 55)	66.7 % (2 of 3)
Methyl	92.6 % (50 of 54)	92.6 % (25 of 27)	92.6 % (25 of 27)

1. cbx7

MHHHHHHSSG RENLYFQGEQ VFAVESIRKK RVRKGKVEYL VKWKGWPPKY STWEPEEHIL DPRLVMAYEE KEE

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		10 mM
2	sodium chloride	natural abundance		300 mM
3	DTT	natural abundance		2 mM
4	D2O			10 %
5	H2O	natural abundance		90 %

LACS Plot; CA

Referencing offset: 0.0 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: 0.0 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: 0.05 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: 0.52 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2K1B, Strand ID: A Detail

Release date

2008-03-04

Citation

Solution NMR structure of the chromobox protein homolog 7
Kaustov, L., Lemak, A., Quyang, H., Gutmanas, A., Fares, C., Bountra, C., Weigelt, J., Ravichandran, M., Loppnau, P., Edwards, A., Min, J., Arrowsmith, C.

Related entities 1. chromobox protein homolog 7, : 1 : 42 entities Detail

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		10 mM
2	sodium chloride	natural abundance		300 mM
3	DTT	natural abundance		2 mM
4	D2O			10 %
5	H2O	natural abundance		90 %

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		10 mM
2	sodium chloride	natural abundance		300 mM
3	DTT	natural abundance		2 mM
4	D2O			10 %
5	H2O	natural abundance		90 %

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		10 mM
2	sodium chloride	natural abundance		300 mM
3	DTT	natural abundance		2 mM
4	D2O			10 %
5	H2O	natural abundance		90 %

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		10 mM
2	sodium chloride	natural abundance		300 mM
3	DTT	natural abundance		2 mM
4	D2O			10 %
5	H2O	natural abundance		90 %

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		10 mM
2	sodium chloride	natural abundance		300 mM
3	DTT	natural abundance		2 mM
4	D2O			10 %
5	H2O	natural abundance		90 %

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		10 mM
2	sodium chloride	natural abundance		300 mM
3	DTT	natural abundance		2 mM
4	D2O			10 %
5	H2O	natural abundance		90 %

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		10 mM
2	sodium chloride	natural abundance		300 mM
3	DTT	natural abundance		2 mM
4	D2O			10 %
5	H2O	natural abundance		90 %

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		10 mM
2	sodium chloride	natural abundance		300 mM
3	DTT	natural abundance		2 mM
4	D2O			10 %
5	H2O	natural abundance		90 %

9 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		10 mM
2	sodium chloride	natural abundance		300 mM
3	DTT	natural abundance		2 mM
4	D2O			10 %
5	H2O	natural abundance		90 %

10 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		10 mM
2	sodium chloride	natural abundance		300 mM
3	DTT	natural abundance		2 mM
4	D2O			10 %
5	H2O	natural abundance		90 %

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		10 mM
2	sodium chloride	natural abundance		300 mM
3	DTT	natural abundance		2 mM
4	D2O			10 %
5	H2O	natural abundance		90 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15674_2k1b.nef
Input source #2: Coordindates	2k1b.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-----
MHHHHHHSSGRENLYFQGEQVFAVESIRKKRVRKGKVEYLVKWKGWPPKYSTWEPEEHILDPRLVMAYEEKEE
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MHHHHHHSSGRENLYFQGEQVFAVESIRKKRVRKGKVEYLVKWKGWPPKYSTWEPEEHILDPRLVMAYEEKEE
--------10--------20--------30--------40--------50--------60--------70---

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	73	0	0	100.0

Content subtype: combined_15674_2k1b.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	659		75.3 (chain: A, length: 73)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	1649 (1)	noe	75.3 (chain: A, length: 73)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	74 (74)	.	67.1 (chain: A, length: 73)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 73, Sequence coverage: 75.3%
- Total number of assignments
  - ¹H chemical shifts: 360
  - ¹³C chemical shifts: 248
  - ¹⁵N chemical shifts: 51
- 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_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 73, Sequence coverage: 75.3%
- Total number of restraints: 1649
- Weight of restraints: 1.0 (1649)
- Potential type of restraints: square-well-parabolic (1649)
- 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_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 73, Sequence coverage: 67.1%
- 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