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BMRB: 17402

2L8D

Structure/function of the LBR Tudor domain

Authors

Liokatis, S., Edlich, C., Soupsana, K., Giannios, I., Sattler, M., Georgatos, S.D., Politou, A.S.

Assembly

LBR Tudor domain

Entity

1. LBR Tudor domain (polymer), 66 monomers, 7481.324 Da Detail

GAMGMPNRKY ADGEVVMGRW PGSVLYYEVQ VTSYDDASHL YTVKYKDGTE LALKESDIRL QSSFKQ

Formula weight

7481.324 Da

Source organism

Exptl. method

Refine. method

simulated annealing, torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 89.4 %, Completeness (bb): 82.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	89.4 % (684 of 765)	97.0 % (385 of 397)	77.6 % (232 of 299)	97.1 % (67 of 69)
Backbone	82.1 % (322 of 392)	97.1 % (132 of 136)	66.7 % (128 of 192)	96.9 % (62 of 64)
Sidechain	97.5 % (422 of 433)	96.9 % (253 of 261)	98.2 % (164 of 167)	100.0 % (5 of 5)
Aromatic	100.0 % (74 of 74)	100.0 % (37 of 37)	100.0 % (36 of 36)	100.0 % (1 of 1)
Methyl	100.0 % (62 of 62)	100.0 % (31 of 31)	100.0 % (31 of 31)

1. LBR Tudor domain

GAMGMPNRKY ADGEVVMGRW PGSVLYYEVQ VTSYDDASHL YTVKYKDGTE LALKESDIRL QSSFKQ

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.9

#	Name	Isotope labeling	Type	Concentration
1	LBR_Tudor_domain			0.8 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM

LACS Plot; CA

Referencing offset: -0.21 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: -0.21 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: -0.05 ppm, Outliers: 3 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 2L8D, Strand ID: A Detail

Release date

2011-12-01

Citation

Solution structure and molecular interactions of lamin B receptor Tudor domain
Liokatis, S., Edlich, C., Soupsana, K., Giannios, I., Panagiotidou, P., Tripsianes, K., Sattler, M., Georgatos, S.D., Politou, A.S.
J. Biol. Chem. (2012), 287, 1032-1042, PubMed 22052904 , DOI 10.1074/jbc.M111.281303 , Abstract

Related entities 1. LBR Tudor domain, : 1 : 1 : 27 entities Detail

Experiments performed 9 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.9

#	Name	Isotope labeling	Type	Concentration
1	LBR_Tudor_domain			0.8 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM

2 2D 1H-13C HSQC

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.9

#	Name	Isotope labeling	Type	Concentration
1	LBR_Tudor_domain			0.8 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM

3 3D CBCA(CO)NH

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.9

#	Name	Isotope labeling	Type	Concentration
1	LBR_Tudor_domain			0.8 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM

4 3D HNCA

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.9

#	Name	Isotope labeling	Type	Concentration
1	LBR_Tudor_domain			0.8 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM

5 3D HNCACB

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.9

#	Name	Isotope labeling	Type	Concentration
1	LBR_Tudor_domain			0.8 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM

6 3D HCCH-TOCSY

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.9

#	Name	Isotope labeling	Type	Concentration
1	LBR_Tudor_domain			0.8 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM

7 3D 1H-15N NOESY

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.9

#	Name	Isotope labeling	Type	Concentration
1	LBR_Tudor_domain			0.8 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM

8 3D 1H-13C NOESY aliphatic

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.9

#	Name	Isotope labeling	Type	Concentration
1	LBR_Tudor_domain			0.8 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM

9 2D 1H-13C HSQC aromatic

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.9

#	Name	Isotope labeling	Type	Concentration
1	LBR_Tudor_domain			0.8 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_17402_2l8d.nef
Input source #2: Coordindates	2l8d.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------
GAMGMPNRKYADGEVVMGRWPGSVLYYEVQVTSYDDASHLYTVKYKDGTELALKESDIRLQSSFKQ
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GAMGMPNRKYADGEVVMGRWPGSVLYYEVQVTSYDDASHLYTVKYKDGTELALKESDIRLQSSFKQ

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	66	0	0	100.0

Content subtype: combined_17402_2l8d.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	687		100.0 (chain: A, length: 66)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	1023 (1)	noe	90.9 (chain: A, length: 66)
2	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	88 (1)	hbond	40.9 (chain: A, length: 66)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 66, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 388
  - ¹³C chemical shifts: 230
  - ¹⁵N chemical shifts: 69
- 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: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 66, Sequence coverage: 90.9%
- Total number of restraints: 1023
- Weight of restraints: 1.0 (1023)
- Potential type of restraints: upper-bound-parabolic (1023)
- Range of distance target values: 2.8, 5.5 (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: DYANA/DIANA_distance_constraints_3
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 66, Sequence coverage: 40.9%
  - Total number of restraints: 88
  - Weight of restraints: 1.0 (88)
  - Potential type of restraints: upper-bound-parabolic (88)
  - Range of distance target values: 1.8, 3.0 (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

Keywords LBR, Protein, Tudor