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BMRB: 17673

2LDM

Not Available

Authors

Cui, G., Botuyan, M., Mer, G.

Assembly

TDRD7

Entity

1. TDRD7 (polymer, Thiol state: not present), 81 monomers, 9054.079 Da Detail

GHMSSEFQIN EQVLASWSDS RFYPAKVTAV NKDGTYTVKF YDGVVQTVKH IHVKAFSKDQ NIVGNARGSR AHSSHLXSKK G

Formula weight

9054.079 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 95.1 %, Completeness: 88.6 %, Completeness (bb): 87.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	88.6 % (818 of 923)	90.6 % (432 of 477)	85.8 % (307 of 358)	89.8 % (79 of 88)
Backbone	87.9 % (420 of 478)	89.1 % (147 of 165)	86.8 % (203 of 234)	88.6 % (70 of 79)
Sidechain	87.3 % (453 of 519)	88.8 % (277 of 312)	84.3 % (167 of 198)	100.0 % (9 of 9)
Aromatic	55.2 % (53 of 96)	60.4 % (29 of 48)	48.9 % (23 of 47)	100.0 % (1 of 1)
Methyl	98.7 % (75 of 76)	97.4 % (37 of 38)	100.0 % (38 of 38)

1. entity

GHMSSEFQIN EQVLASWSDS RFYPAKVTAV NKDGTYTVKF YDGVVQTVKH IHVKAFSKDQ NIVGNARGSR AHSSHLXSKK G

Show sample condition

Sample #1

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

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		25 mM
3	DSS	natural abundance		0.3 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

Sample #2

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

#	Name	Isotope labeling	Type	Concentration
6	entity	[U-100% 13C; U-100% 15N]		1 mM
7	sodium phosphate	natural abundance		25 mM
8	DSS	natural abundance		0.3 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

LACS Plot; CA

Referencing offset: -0.1 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: -0.1 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: -0.02 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: 0.42 ppm, Outliers: 3 Detail

Protein Blocks Logo

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

Release date

2012-05-08

Citation

PHF20 is an effector protein of p53 double lysine methylation that stabilizes and activates p53
Cui, G., Park, S., Badeaux, A.I., Kim, D., Lee, J., Thompson, J.R., Yan, F., Kaneko, S., Yuan, Z., Botuyan, M.V., Bedford, M.T., Cheng, J.Q., Mer, G.
Nat. Struct. Mol. Biol. (2012), 19, 916-924, PubMed 22864287 , DOI 10.1038/nsmb.2353 , Abstract

Related entities 1. TDRD7, : 1 : 1 : 21 entities Detail

Experiments performed 15 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 700 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	entity	[U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		25 mM
3	DSS	natural abundance		0.3 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 700 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
6	entity	[U-100% 13C; U-100% 15N]		1 mM
7	sodium phosphate	natural abundance		25 mM
8	DSS	natural abundance		0.3 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

3 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 700 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
6	entity	[U-100% 13C; U-100% 15N]		1 mM
7	sodium phosphate	natural abundance		25 mM
8	DSS	natural abundance		0.3 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

4 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 700 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
6	entity	[U-100% 13C; U-100% 15N]		1 mM
7	sodium phosphate	natural abundance		25 mM
8	DSS	natural abundance		0.3 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

5 3D HNCACB

Instrument

Bruker Avance - 700 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
6	entity	[U-100% 13C; U-100% 15N]		1 mM
7	sodium phosphate	natural abundance		25 mM
8	DSS	natural abundance		0.3 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

6 3D CBCA(CO)NH

Instrument

Bruker Avance - 700 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
6	entity	[U-100% 13C; U-100% 15N]		1 mM
7	sodium phosphate	natural abundance		25 mM
8	DSS	natural abundance		0.3 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

7 3D HBHA(CO)NH

Instrument

Bruker Avance - 700 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
6	entity	[U-100% 13C; U-100% 15N]		1 mM
7	sodium phosphate	natural abundance		25 mM
8	DSS	natural abundance		0.3 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

8 3D HN(CA)CO

Instrument

Bruker Avance - 700 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
6	entity	[U-100% 13C; U-100% 15N]		1 mM
7	sodium phosphate	natural abundance		25 mM
8	DSS	natural abundance		0.3 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

9 3D CCH-TOCSY

Instrument

Bruker Avance - 700 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
6	entity	[U-100% 13C; U-100% 15N]		1 mM
7	sodium phosphate	natural abundance		25 mM
8	DSS	natural abundance		0.3 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

10 2D (HB)CB(CGCD)HD

Instrument

Bruker Avance - 700 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
6	entity	[U-100% 13C; U-100% 15N]		1 mM
7	sodium phosphate	natural abundance		25 mM
8	DSS	natural abundance		0.3 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

11 2D (HB)CB(CGCDCE)HE

Instrument

Bruker Avance - 700 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
6	entity	[U-100% 13C; U-100% 15N]		1 mM
7	sodium phosphate	natural abundance		25 mM
8	DSS	natural abundance		0.3 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

12 3D 1H-15N NOESY

Instrument

Bruker Avance - 700 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	entity	[U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		25 mM
3	DSS	natural abundance		0.3 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

13 3D 1H-15N NOESY

Instrument

Bruker Avance - 700 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
6	entity	[U-100% 13C; U-100% 15N]		1 mM
7	sodium phosphate	natural abundance		25 mM
8	DSS	natural abundance		0.3 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

14 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 700 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
6	entity	[U-100% 13C; U-100% 15N]		1 mM
7	sodium phosphate	natural abundance		25 mM
8	DSS	natural abundance		0.3 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

15 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 700 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
6	entity	[U-100% 13C; U-100% 15N]		1 mM
7	sodium phosphate	natural abundance		25 mM
8	DSS	natural abundance		0.3 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

NMR combined restraints 8 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_17673_2ldm.nef
Input source #2: Coordindates	2ldm.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	True (see coodinates for details)
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)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:76:LEU:C	1:77:M2L:N	unknown	unknown	n/a
1:77:M2L:C	1:78:SER:N	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	370	M2L	(2R)-2-amino-3-(2-dimethylaminoethylsulfanyl)propanoic acid	Coordinates

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------90-------100-------110-------120-------130-------140-----200------370----
GHMSSEFQINEQVLASWSDSRFYPAKVTAVNKDGTYTVKFYDGVVQTVKHIHVKAFSKDQNIVGNARGSRAHSSHLXSKKG
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GHMSSEFQINEQVLASWSDSRFYPAKVTAVNKDGTYTVKFYDGVVQTVKHIHVKAFSKDQNIVGNARGSRAHSSHLXSKKG
--------10--------20--------30--------40--------50--------60--------70--------80-

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	81	0	0	100.0

Content subtype: combined_17673_2ldm.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	2		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	823		95.1 (chain: A, length: 81)
1	Distance restraints	AMBER_distance_constraints_3	Warning	91 (1)	noe	48.1 (chain: A, length: 81)
2	Distance restraints	AMBER_distance_constraints_5	Warning	365 (1)	noe	60.5 (chain: A, length: 81)
3	Distance restraints	AMBER_distance_constraints_7	Warning	5955 (1)	noe	93.8 (chain: A, length: 81)
1	Dihedral angle restraints	AMBER_dihedral_2	Warning	2 (2)	.	2.5 (chain: A, length: 81)
2	Dihedral angle restraints	AMBER_dihedral_4	Warning	1 (1)	.	1.2 (chain: A, length: 81)
3	Dihedral angle restraints	AMBER_dihedral_6	OK	105 (105)	.	63.0 (chain: A, length: 81)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 81, Sequence coverage: 95.1%
- Total number of assignments
  - ¹H chemical shifts: 439
  - ¹³C chemical shifts: 306
  - ¹⁵N chemical shifts: 78
- 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

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: AMBER_distance_constraints_3
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 81, Sequence coverage: 48.1%
- Total number of restraints: 90
- Weight of restraints: 1.0 (90)
- Potential type of restraints: square-well-parabolic (90)
- Range of distance target values: 2.25, 5.36 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: AMBER_distance_constraints_5
  - Status: Warning
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 81, Sequence coverage: 60.5%
  - Total number of restraints: 353
  - Weight of restraints: 1.0 (353)
  - Potential type of restraints: square-well-parabolic (353)
  - Range of distance target values: 2.55, 6.83 (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: AMBER_distance_constraints_7
    - Status: Warning
    - Experiment type: noe
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 81, Sequence coverage: 93.8%
    - Total number of restraints: 5749
    - Weight of restraints: 1.0 (5749)
    - Potential type of restraints: square-well-parabolic (5749)
    - Range of distance target values: 2.55, 7.61 (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: AMBER_dihedral_2
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 81, Sequence coverage: 2.5%
- Total number of restraints: 2
- Total number of restraints per polymer type: 2
- Weight of restraints: 1.0 (2)
- Potential type of restraints: square-well-parabolic (2)
- Dihedral angle restraints per residue
- Saveframe: AMBER_dihedral_4
  - Status: Warning
  - Experiment type: .
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 81, Sequence coverage: 1.2%
  - Total number of restraints: 1
  - Total number of restraints per polymer type: 1
  - Weight of restraints: 1.0 (1)
  - Potential type of restraints: square-well-parabolic (1)
  - Dihedral angle restraints per residue
  - Saveframe: AMBER_dihedral_6
    - Status: OK
    - Experiment type: .
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 81, Sequence coverage: 63.0%
    - Total number of restraints: 105
    - Total number of restraints per polymer type: 105
    - Weight of restraints: 1.0 (105)
    - Potential type of restraints: square-well-parabolic (105)
    - Plot of Phi-Psi angle restraints
    - Dihedral angle restraints per residue
      - Chain_ID: A

Keywords Epigenetics, Methylated lysine analogue, Methylated p53, PHF20, Protein, Tudor domain