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BMRB: 19710

2MJ8

Solution structure of CDYL2 chromodomain

Authors

Qin, S., Houliston, S., Arrowsmith, C.H., Edwards, A.M., Wu, H., Min, J.

Assembly

CDYL2 chromodomain

Entity

1. CDYL2 chromodomain (polymer), 64 monomers, 7680.472 Da Detail

GASGDLYEVE RIVDKRKNKK GKWEYLIRWK GYGSTEDTWE PEHHLLHCEE FIDEFNGLHM SKDK

Formula weight

7680.472 Da

Source organism

Escherichia coli

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 95.3 %, Completeness: 77.4 %, Completeness (bb): 89.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	77.4 % (608 of 786)	77.3 % (320 of 414)	77.0 % (234 of 304)	79.4 % (54 of 68)
Backbone	89.5 % (342 of 382)	88.7 % (118 of 133)	91.4 % (170 of 186)	85.7 % (54 of 63)
Sidechain	69.5 % (321 of 462)	71.9 % (202 of 281)	67.6 % (119 of 176)	0.0 % (0 of 5)
Aromatic	3.1 % (3 of 96)	4.2 % (2 of 48)	2.2 % (1 of 45)	0.0 % (0 of 3)
Methyl	95.7 % (44 of 46)	95.7 % (22 of 23)	95.7 % (22 of 23)

1. entity

GASGDLYEVE RIVDKRKNKK GKWEYLIRWK GYGSTEDTWE PEHHLLHCEE FIDEFNGLHM SKDK

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	TRIS	natural abundance		20 mM
2	sodium chloride	natural abundance		150 mM
3	DTT	natural abundance		2 mM
4	H2O	natural abundance		90 %
5	D2O	[U-100% 2H]		10 %

LACS Plot; CA

Referencing offset: 0.05 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: 0.05 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: 0.06 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: 0.11 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2MJ8, Strand ID: A Detail

Release date

2014-04-21

Citation

Solution structure of CDYL2 chromodomain
Qin, S., Houliston, S., Arrowsmith, C.H., Wu, H., Min, J.
Not known

Related entities 1. CDYL2 chromodomain, : 1 : 4 : 6 : 69 entities Detail

Interaction partners 1. CDYL2 chromodomain, : 7 interactors Detail

More details for 7 interactors identified by 2 citations

Experiments performed 10 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 7.5

#	Name	Isotope labeling	Type	Concentration
1	TRIS	natural abundance		20 mM
2	sodium chloride	natural abundance		150 mM
3	DTT	natural abundance		2 mM
4	H2O	natural abundance		90 %
5	D2O	[U-100% 2H]		10 %

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 7.5

#	Name	Isotope labeling	Type	Concentration
1	TRIS	natural abundance		20 mM
2	sodium chloride	natural abundance		150 mM
3	DTT	natural abundance		2 mM
4	H2O	natural abundance		90 %
5	D2O	[U-100% 2H]		10 %

3 3D HNCO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	TRIS	natural abundance		20 mM
2	sodium chloride	natural abundance		150 mM
3	DTT	natural abundance		2 mM
4	H2O	natural abundance		90 %
5	D2O	[U-100% 2H]		10 %

4 3D HNCA

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	TRIS	natural abundance		20 mM
2	sodium chloride	natural abundance		150 mM
3	DTT	natural abundance		2 mM
4	H2O	natural abundance		90 %
5	D2O	[U-100% 2H]		10 %

5 3D CBCA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	TRIS	natural abundance		20 mM
2	sodium chloride	natural abundance		150 mM
3	DTT	natural abundance		2 mM
4	H2O	natural abundance		90 %
5	D2O	[U-100% 2H]		10 %

6 3D HBHA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	TRIS	natural abundance		20 mM
2	sodium chloride	natural abundance		150 mM
3	DTT	natural abundance		2 mM
4	H2O	natural abundance		90 %
5	D2O	[U-100% 2H]		10 %

7 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 7.5

#	Name	Isotope labeling	Type	Concentration
1	TRIS	natural abundance		20 mM
2	sodium chloride	natural abundance		150 mM
3	DTT	natural abundance		2 mM
4	H2O	natural abundance		90 %
5	D2O	[U-100% 2H]		10 %

8 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	TRIS	natural abundance		20 mM
2	sodium chloride	natural abundance		150 mM
3	DTT	natural abundance		2 mM
4	H2O	natural abundance		90 %
5	D2O	[U-100% 2H]		10 %

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 7.5

#	Name	Isotope labeling	Type	Concentration
1	TRIS	natural abundance		20 mM
2	sodium chloride	natural abundance		150 mM
3	DTT	natural abundance		2 mM
4	H2O	natural abundance		90 %
5	D2O	[U-100% 2H]		10 %

10 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	TRIS	natural abundance		20 mM
2	sodium chloride	natural abundance		150 mM
3	DTT	natural abundance		2 mM
4	H2O	natural abundance		90 %
5	D2O	[U-100% 2H]		10 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19710_2mj8.nef
Input source #2: Coordindates	2mj8.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----
GASGDLYEVERIVDKRKNKKGKWEYLIRWKGYGSTEDTWEPEHHLLHCEEFIDEFNGLHMSKDK
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GASGDLYEVERIVDKRKNKKGKWEYLIRWKGYGSTEDTWEPEHHLLHCEEFIDEFNGLHMSKDK

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	64	0	0	100.0

Content subtype: combined_19710_2mj8.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	608		95.3 (chain: A, length: 64)
1	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	1713 (1)	noe	93.8 (chain: A, length: 64)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	64 (1)	hbond	60.9 (chain: A, length: 64)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	88 (88)	.	84.4 (chain: A, length: 64)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 64, Sequence coverage: 95.3%
- Total number of assignments
  - ¹H chemical shifts: 322
  - ¹³C chemical shifts: 232
  - ¹⁵N chemical shifts: 54
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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: CNS/XPLOR_distance_constraints_4
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 64, Sequence coverage: 93.8%
- Total number of restraints: 1713
- Weight of restraints: 1.0 (1713)
- Potential type of restraints: square-well-parabolic (1713)
- Range of distance target values: 2.25, 4.4 (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
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 64, Sequence coverage: 60.9%
  - Total number of restraints: 64
  - Weight of restraints: 1.0 (64)
  - Potential type of restraints: square-well-parabolic (64)
  - Range of distance target values: 2.05, 3.0 (Å)
  - Histogram of 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: 64, Sequence coverage: 84.4%
- Total number of restraints: 88
- Total number of restraints per polymer type: 88
- Weight of restraints: 1.0 (88)
- Potential type of restraints: square-well-parabolic (88)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords chromodomain