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BMRB: 18455

2LSY

Structure of the C-terminal domain from human REV1

Authors

Pozhidaeva, A., Pustovalova, Y., Bezsonova, I., Korzhnev, D.

Assembly

REV1-CT

Entity

1. REV1-CT (polymer, Thiol state: all free), 95 monomers, 11002.59 Da Detail

GNLAGAVEFN DVKTLLREWI TTISDPMEED ILQVVKYCTD LIEEKDLEKL DLVIKYMKRL MQQSVESVWN MAFDFILDNV QVVLQQTYGS TLKVT

Formula weight

11002.59 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.9 %, Completeness: 89.6 %, Completeness (bb): 95.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	89.6 % (1030 of 1150)	90.4 % (536 of 593)	86.9 % (392 of 451)	96.2 % (102 of 106)
Backbone	95.2 % (541 of 568)	95.3 % (183 of 192)	95.0 % (268 of 282)	95.7 % (90 of 94)
Sidechain	85.6 % (577 of 674)	88.0 % (353 of 401)	81.2 % (212 of 261)	100.0 % (12 of 12)
Aromatic	55.1 % (43 of 78)	66.7 % (26 of 39)	40.5 % (15 of 37)	100.0 % (2 of 2)
Methyl	88.2 % (120 of 136)	88.2 % (60 of 68)	88.2 % (60 of 68)

1. entity

GNLAGAVEFN DVKTLLREWI TTISDPMEED ILQVVKYCTD LIEEKDLEKL DLVIKYMKRL MQQSVESVWN MAFDFILDNV QVVLQQTYGS TLKVT

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	REV1-CT	[U-99% 13C; U-99% 15N]		0.9 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		100 mM
4	EDTA	natural abundance		0.25 mM
5	DTT	natural abundance		5 mM
6	sodium azide	natural abundance		0.05 %
7	H2O	natural abundance		90 %
8	D2O	[U-2H]		10 %

LACS Plot; CA

Referencing offset: -0.23 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: -0.23 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: 0.1 ppm, Outliers: 2 Detail

LACS Plot; CO

Referencing offset: -0.12 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2012-12-17

Citation

NMR structure and dynamics of the C-terminal domain from human Rev1 and its complex with Rev1 interacting region of DNA polymerase η
Pozhidaeva, A., Pustovalova, Y., Bezsonova, S., Walker, I., Korzhnev, G.C.
Biochemistry (2012), 51, 5506-5520, PubMed 22691049 , DOI 10.1021/bi300566z , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 18434 released on 2012-06-17
Title C-terminal domain of human REV1 in complex with DNA-polymerase H (eta)

Related entities 1. REV1-CT, : 1 : 3 : 10 : 13 entities Detail

Interaction partners 1. REV1-CT, : 3 interactors Detail

More details for 3 interactors identified by 2 citations

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	REV1-CT	[U-99% 13C; U-99% 15N]		0.9 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		100 mM
4	EDTA	natural abundance		0.25 mM
5	DTT	natural abundance		5 mM
6	sodium azide	natural abundance		0.05 %
7	H2O	natural abundance		90 %
8	D2O	[U-2H]		10 %

2 3D HNCO

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	REV1-CT	[U-99% 13C; U-99% 15N]		0.9 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		100 mM
4	EDTA	natural abundance		0.25 mM
5	DTT	natural abundance		5 mM
6	sodium azide	natural abundance		0.05 %
7	H2O	natural abundance		90 %
8	D2O	[U-2H]		10 %

3 3D HNCACB

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	REV1-CT	[U-99% 13C; U-99% 15N]		0.9 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		100 mM
4	EDTA	natural abundance		0.25 mM
5	DTT	natural abundance		5 mM
6	sodium azide	natural abundance		0.05 %
7	H2O	natural abundance		90 %
8	D2O	[U-2H]		10 %

4 3D HNCA

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	REV1-CT	[U-99% 13C; U-99% 15N]		0.9 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		100 mM
4	EDTA	natural abundance		0.25 mM
5	DTT	natural abundance		5 mM
6	sodium azide	natural abundance		0.05 %
7	H2O	natural abundance		90 %
8	D2O	[U-2H]		10 %

5 3D 1H-15N NOESY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	REV1-CT	[U-99% 13C; U-99% 15N]		0.9 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		100 mM
4	EDTA	natural abundance		0.25 mM
5	DTT	natural abundance		5 mM
6	sodium azide	natural abundance		0.05 %
7	H2O	natural abundance		90 %
8	D2O	[U-2H]		10 %

6 2D 1H-13C HSQC aliphatic

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	REV1-CT	[U-99% 13C; U-99% 15N]		0.9 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		100 mM
4	EDTA	natural abundance		0.25 mM
5	DTT	natural abundance		5 mM
6	sodium azide	natural abundance		0.05 %
7	H2O	natural abundance		90 %
8	D2O	[U-2H]		10 %

7 2D 1H-13C HSQC aromatic

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	REV1-CT	[U-99% 13C; U-99% 15N]		0.9 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		100 mM
4	EDTA	natural abundance		0.25 mM
5	DTT	natural abundance		5 mM
6	sodium azide	natural abundance		0.05 %
7	H2O	natural abundance		90 %
8	D2O	[U-2H]		10 %

8 3D 1H-13C NOESY aromatic

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	REV1-CT	[U-99% 13C; U-99% 15N]		0.9 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		100 mM
4	EDTA	natural abundance		0.25 mM
5	DTT	natural abundance		5 mM
6	sodium azide	natural abundance		0.05 %
7	H2O	natural abundance		90 %
8	D2O	[U-2H]		10 %

9 3D 1H-13C NOESY aliphatic

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	REV1-CT	[U-99% 13C; U-99% 15N]		0.9 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		100 mM
4	EDTA	natural abundance		0.25 mM
5	DTT	natural abundance		5 mM
6	sodium azide	natural abundance		0.05 %
7	H2O	natural abundance		90 %
8	D2O	[U-2H]		10 %

10 3D HBHA(CO)NH

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	REV1-CT	[U-99% 13C; U-99% 15N]		0.9 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		100 mM
4	EDTA	natural abundance		0.25 mM
5	DTT	natural abundance		5 mM
6	sodium azide	natural abundance		0.05 %
7	H2O	natural abundance		90 %
8	D2O	[U-2H]		10 %

11 3D HCCH-TOCSY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	REV1-CT	[U-99% 13C; U-99% 15N]		0.9 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		100 mM
4	EDTA	natural abundance		0.25 mM
5	DTT	natural abundance		5 mM
6	sodium azide	natural abundance		0.05 %
7	H2O	natural abundance		90 %
8	D2O	[U-2H]		10 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18455_2lsy.nef
Input source #2: Coordindates	2lsy.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

---1160---1170------1180------1190------1200------1210------1220------1230------1240------1250-
GNLAGAVEFNDVKTLLREWITTISDPMEEDILQVVKYCTDLIEEKDLEKLDLVIKYMKRLMQQSVESVWNMAFDFILDNVQVVLQQTYGSTLKVT
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GNLAGAVEFNDVKTLLREWITTISDPMEEDILQVVKYCTDLIEEKDLEKLDLVIKYMKRLMQQSVESVWNMAFDFILDNVQVVLQQTYGSTLKVT
--------10--------20--------30--------40--------50--------60--------70--------80--------90-----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	95	0	0	100.0

Content subtype: combined_18455_2lsy.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1002		96.8 (chain: A, length: 95)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	2609 (1)	noe	97.9 (chain: A, length: 95)
2	Distance restraints	DYANA/DIANA_distance_constraints_5	OK	92 (1)	hbond	66.3 (chain: A, length: 95)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_4	Warning	447 (447)	.	92.6 (chain: A, length: 95)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 95, Sequence coverage: 96.8%
- Total number of assignments
  - ¹H chemical shifts: 524
  - ¹³C chemical shifts: 380
  - ¹⁵N chemical shifts: 98
- 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: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 95, Sequence coverage: 97.9%
- Total number of restraints: 2608
- Weight of restraints: 1.0 (2608)
- Potential type of restraints: upper-bound-parabolic (2608)
- Range of distance target values: 2.38, 5.74 (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_5
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 95, Sequence coverage: 66.3%
  - Total number of restraints: 92
  - Weight of restraints: 1.0 (92)
  - Potential type of restraints: upper-bound-parabolic (92)
  - Range of distance target values: 2.0, 3.0 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_4
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 95, Sequence coverage: 92.6%
- Total number of restraints: 447
- Total number of restraints per polymer type: 447
- Weight of restraints: 1.0 (447)
- Potential type of restraints: square-well-parabolic (447)
- Plot of Chi1-Chi2 angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords DNA polymerase, DNA repair, translesion synthesis