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BMRB: 17607

2MAM

Solution structure of RBBP1 tudor domain

Authors

Gong, W., Feng, Y.

Assembly

RBBP1 tudor domain

Entity

1. RBBP1 tudor domain (polymer), 118 monomers, 13153.70 Da Detail

ADEPAYLTVG TDVSAKYRGA FCEAKIKTVK RLVKVKVLLK QDNTTQLVQD DQVKGPLRVG AIVETRTSDG SFQEAIISKL TDASWYTVVF DDGDERTLRR TSLCLKGERH FAESETLD

Formula weight

13153.7 Da

Source organism

Exptl. method

Refine. method

simulated annealing, torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 99.2 %, Completeness: 88.2 %, Completeness (bb): 95.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	88.2 % (1191 of 1350)	83.8 % (584 of 697)	92.6 % (491 of 530)	94.3 % (116 of 123)
Backbone	95.5 % (672 of 704)	95.0 % (229 of 241)	96.3 % (334 of 347)	94.0 % (109 of 116)
Sidechain	83.0 % (628 of 757)	77.9 % (355 of 456)	90.5 % (266 of 294)	100.0 % (7 of 7)
Aromatic	80.0 % (64 of 80)	80.0 % (32 of 40)	79.5 % (31 of 39)	100.0 % (1 of 1)
Methyl	96.0 % (144 of 150)	96.0 % (72 of 75)	96.0 % (72 of 75)

1. entity

ADEPAYLTVG TDVSAKYRGA FCEAKIKTVK RLVKVKVLLK QDNTTQLVQD DQVKGPLRVG AIVETRTSDG SFQEAIISKL TDASWYTVVF DDGDERTLRR TSLCLKGERH FAESETLD

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	RBBP1	[U-95% 15N]		0.6 mM
2	TRIS	natural abundance		50 mM
3	DTT	natural abundance		5 mM
4	sodium chloride	natural abundance		50 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
7	RBBP1	[U-95% 13C; U-95% 15N]		0.6 mM
8	TRIS	natural abundance		50 mM
9	DTT	natural abundance		5 mM
10	sodium chloride	natural abundance		50 mM
11	H2O	natural abundance		90 %
12	D2O	natural abundance		10 %

LACS Plot; CA

Referencing offset: -0.16 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: -0.16 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: -0.11 ppm, Outliers: 3 Detail

LACS Plot; CO

Referencing offset: 0.42 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2012-05-08

Citation

Structural insight into recognition of methylated histone tails by retinoblastoma-binding protein 1
Gong, W., Zhou, T., Mo, J., Perrett, S., Wang, J., Feng, Y.
J. Biol. Chem. (2012), 287, 8531-8540, PubMed 22247551 , DOI 10.1074/jbc.M111.299149 , Abstract

Related entities 1. RBBP1 tudor domain, : 1 : 2 : 2 : 13 entities Detail

Interaction partners 1. RBBP1 tudor domain, : 10 interactors Detail

More details for 10 interactors identified by 5 citations

Experiments performed 14 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker DMX - 600 MHz equipped with a z-gradient triple-resonance cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	RBBP1	[U-95% 15N]		0.6 mM
2	TRIS	natural abundance		50 mM
3	DTT	natural abundance		5 mM
4	sodium chloride	natural abundance		50 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

2 2D 1H-13C HSQC

Instrument

Bruker DMX - 600 MHz equipped with a z-gradient triple-resonance cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
7	RBBP1	[U-95% 13C; U-95% 15N]		0.6 mM
8	TRIS	natural abundance		50 mM
9	DTT	natural abundance		5 mM
10	sodium chloride	natural abundance		50 mM
11	H2O	natural abundance		90 %
12	D2O	natural abundance		10 %

3 2D 1H-13C HSQC aromatic

Instrument

Bruker DMX - 600 MHz equipped with a z-gradient triple-resonance cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
7	RBBP1	[U-95% 13C; U-95% 15N]		0.6 mM
8	TRIS	natural abundance		50 mM
9	DTT	natural abundance		5 mM
10	sodium chloride	natural abundance		50 mM
11	H2O	natural abundance		90 %
12	D2O	natural abundance		10 %

4 3D CBCA(CO)NH

Instrument

Bruker DMX - 600 MHz equipped with a z-gradient triple-resonance cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
7	RBBP1	[U-95% 13C; U-95% 15N]		0.6 mM
8	TRIS	natural abundance		50 mM
9	DTT	natural abundance		5 mM
10	sodium chloride	natural abundance		50 mM
11	H2O	natural abundance		90 %
12	D2O	natural abundance		10 %

5 3D HNCACB

Instrument

Bruker DMX - 600 MHz equipped with a z-gradient triple-resonance cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
7	RBBP1	[U-95% 13C; U-95% 15N]		0.6 mM
8	TRIS	natural abundance		50 mM
9	DTT	natural abundance		5 mM
10	sodium chloride	natural abundance		50 mM
11	H2O	natural abundance		90 %
12	D2O	natural abundance		10 %

6 3D HNCO

Instrument

Bruker DMX - 600 MHz equipped with a z-gradient triple-resonance cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
7	RBBP1	[U-95% 13C; U-95% 15N]		0.6 mM
8	TRIS	natural abundance		50 mM
9	DTT	natural abundance		5 mM
10	sodium chloride	natural abundance		50 mM
11	H2O	natural abundance		90 %
12	D2O	natural abundance		10 %

7 3D HCACO

Instrument

Bruker DMX - 600 MHz equipped with a z-gradient triple-resonance cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
7	RBBP1	[U-95% 13C; U-95% 15N]		0.6 mM
8	TRIS	natural abundance		50 mM
9	DTT	natural abundance		5 mM
10	sodium chloride	natural abundance		50 mM
11	H2O	natural abundance		90 %
12	D2O	natural abundance		10 %

8 3D 1H-15N TOCSY

Instrument

Bruker DMX - 600 MHz equipped with a z-gradient triple-resonance cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	RBBP1	[U-95% 15N]		0.6 mM
2	TRIS	natural abundance		50 mM
3	DTT	natural abundance		5 mM
4	sodium chloride	natural abundance		50 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

9 3D HBHA(CO)NH

Instrument

Bruker DMX - 600 MHz equipped with a z-gradient triple-resonance cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	RBBP1	[U-95% 15N]		0.6 mM
2	TRIS	natural abundance		50 mM
3	DTT	natural abundance		5 mM
4	sodium chloride	natural abundance		50 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

10 3D HCCH-TOCSY

Instrument

Bruker DMX - 600 MHz equipped with a z-gradient triple-resonance cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
7	RBBP1	[U-95% 13C; U-95% 15N]		0.6 mM
8	TRIS	natural abundance		50 mM
9	DTT	natural abundance		5 mM
10	sodium chloride	natural abundance		50 mM
11	H2O	natural abundance		90 %
12	D2O	natural abundance		10 %

11 3D 1H-15N NOESY

Instrument

Bruker DMX - 600 MHz equipped with a z-gradient triple-resonance cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	RBBP1	[U-95% 15N]		0.6 mM
2	TRIS	natural abundance		50 mM
3	DTT	natural abundance		5 mM
4	sodium chloride	natural abundance		50 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

12 3D 1H-13C NOESY

Instrument

Bruker DMX - 600 MHz equipped with a z-gradient triple-resonance cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
7	RBBP1	[U-95% 13C; U-95% 15N]		0.6 mM
8	TRIS	natural abundance		50 mM
9	DTT	natural abundance		5 mM
10	sodium chloride	natural abundance		50 mM
11	H2O	natural abundance		90 %
12	D2O	natural abundance		10 %

13 3D 1H-13C NOESY aromatic

Instrument

Bruker DMX - 600 MHz equipped with a z-gradient triple-resonance cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
7	RBBP1	[U-95% 13C; U-95% 15N]		0.6 mM
8	TRIS	natural abundance		50 mM
9	DTT	natural abundance		5 mM
10	sodium chloride	natural abundance		50 mM
11	H2O	natural abundance		90 %
12	D2O	natural abundance		10 %

14 3D HCCH-COSY

Instrument

Bruker DMX - 600 MHz equipped with a z-gradient triple-resonance cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
7	RBBP1	[U-95% 13C; U-95% 15N]		0.6 mM
8	TRIS	natural abundance		50 mM
9	DTT	natural abundance		5 mM
10	sodium chloride	natural abundance		50 mM
11	H2O	natural abundance		90 %
12	D2O	natural abundance		10 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_17607_2mam.nef
Input source #2: Coordindates	2mam.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
ADEPAYLTVGTDVSAKYRGAFCEAKIKTVKRLVKVKVLLKQDNTTQLVQDDQVKGPLRVGAIVETRTSDGSFQEAIISKLTDASWYTVVFDDGDERTLRR
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ADEPAYLTVGTDVSAKYRGAFCEAKIKTVKRLVKVKVLLKQDNTTQLVQDDQVKGPLRVGAIVETRTSDGSFQEAIISKLTDASWYTVVFDDGDERTLRR

-------110--------
TSLCLKGERHFAESETLD
||||||||||||||||||
TSLCLKGERHFAESETLD

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_17607_2mam.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1179		99.2 (chain: A, length: 118)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	8293 (1)	noe	97.5 (chain: A, length: 118)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	52 (1)	hbond	25.4 (chain: A, length: 118)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	170 (170)	.	87.3 (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: 99.2%
- Total number of assignments
  - ¹H chemical shifts: 575
  - ¹³C chemical shifts: 488
  - ¹⁵N chemical shifts: 116
- 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_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 118, Sequence coverage: 97.5%
- Total number of restraints: 8202
- Weight of restraints: 1.0 (8202)
- Potential type of restraints: square-well-parabolic (8202)
- 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: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 118, Sequence coverage: 25.4%
  - Total number of restraints: 52
  - Weight of restraints: 1.0 (52)
  - Potential type of restraints: square-well-parabolic (52)
  - Range of distance target values: 1.95, 2.9 (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_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 118, Sequence coverage: 87.3%
- Total number of restraints: 170
- Total number of restraints per polymer type: 170
- Weight of restraints: 1.0 (170)
- Potential type of restraints: square-well-parabolic (170)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords RBBP1, tudor domain