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BMRB: 15325

2JRB

C-terminal domain of ORF1p from mouse LINE-1

Authors

Januszyk, K., Clubb, R.

Assembly

CTD

Entity

1. CTD (polymer, Thiol state: all free), 88 monomers, 10410.96 Da Detail

MQVTYKGRPI RITPDFSPET MKARRAWTDV IQTLREHKCQ PRLLYPAKLS ITIDGETKVF HDKTKFTQYL STNPALQRII TEKKQYKD

Formula weight

10410.96 Da

Source organism

Exptl. method

Refine. method

DGSA-distance geometry simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 93.5 %, Completeness (bb): 97.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	93.5 % (1029 of 1100)	91.2 % (531 of 582)	96.5 % (413 of 428)	94.4 % (85 of 90)
Backbone	97.5 % (503 of 516)	96.5 % (166 of 172)	98.1 % (257 of 262)	97.6 % (80 of 82)
Sidechain	91.3 % (612 of 670)	89.0 % (365 of 410)	96.0 % (242 of 252)	62.5 % (5 of 8)
Aromatic	87.8 % (72 of 82)	87.8 % (36 of 41)	87.5 % (35 of 40)	100.0 % (1 of 1)
Methyl	96.8 % (91 of 94)	95.7 % (45 of 47)	97.9 % (46 of 47)

1. CTD

MQVTYKGRPI RITPDFSPET MKARRAWTDV IQTLREHKCQ PRLLYPAKLS ITIDGETKVF HDKTKFTQYL STNPALQRII TEKKQYKD

Show sample condition

Sample

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 300 K, pH 6.5, Details Phosphate buffer, pH=6.5 200 mM NaCl 5.0 mM DTT

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1 mM
2	Phosphate buffer			50 mM
3	NaCl			200 mM
4	DTT			5 mM
5	D2O			7 %

LACS Plot; CA

Referencing offset: -0.15 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: -0.15 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: 0.01 ppm, Outliers: 3 Detail

LACS Plot; CO

Referencing offset: 0.15 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 40 models in PDB: 2JRB, Strand ID: A Detail

Release date

2007-07-23

Citation

Identification and solution structure of a highly conserved C-terminal domain within ORF1p required for retrotransposition of long interspersed nuclear element-1
Januszyk, K., Li, P.W., Villareal, V., Branciforte, D., Wu, H., Xie, Y., Feigon, J., Loo, J.A., Martin, S.L., Clubb, R.T.
J. Biol. Chem. (2007), 282, 24893-24904, PubMed 17569664 , DOI 10.1074/jbc.M702023200 , Abstract

Entries sharing articles Swiss-Prot: 1 entries Detail

Swiss-Prot: P11260 released on 1989-07-01
Title LORF1_MOUSE Entity LINE-1 retrotransposable element ORF1 protein

Related entities 1. CTD, : 1 : 2 : 47 entities Detail

Experiments performed 16 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 300 K, pH 6.5, Details Phosphate buffer, pH=6.5 200 mM NaCl 5.0 mM DTT

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1 mM
2	Phosphate buffer			50 mM
3	NaCl			200 mM
4	DTT			5 mM
5	D2O			7 %

2 2D 1H-13C HSQC

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 300 K, pH 6.5, Details Phosphate buffer, pH=6.5 200 mM NaCl 5.0 mM DTT

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1 mM
2	Phosphate buffer			50 mM
3	NaCl			200 mM
4	DTT			5 mM
5	D2O			7 %

3 3D CBCA(CO)NH

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 300 K, pH 6.5, Details Phosphate buffer, pH=6.5 200 mM NaCl 5.0 mM DTT

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1 mM
2	Phosphate buffer			50 mM
3	NaCl			200 mM
4	DTT			5 mM
5	D2O			7 %

4 3D C(CO)NH

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 300 K, pH 6.5, Details Phosphate buffer, pH=6.5 200 mM NaCl 5.0 mM DTT

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1 mM
2	Phosphate buffer			50 mM
3	NaCl			200 mM
4	DTT			5 mM
5	D2O			7 %

5 3D HNCO

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 300 K, pH 6.5, Details Phosphate buffer, pH=6.5 200 mM NaCl 5.0 mM DTT

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1 mM
2	Phosphate buffer			50 mM
3	NaCl			200 mM
4	DTT			5 mM
5	D2O			7 %

6 3D HNCA

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 300 K, pH 6.5, Details Phosphate buffer, pH=6.5 200 mM NaCl 5.0 mM DTT

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1 mM
2	Phosphate buffer			50 mM
3	NaCl			200 mM
4	DTT			5 mM
5	D2O			7 %

7 3D HNCACB

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 300 K, pH 6.5, Details Phosphate buffer, pH=6.5 200 mM NaCl 5.0 mM DTT

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1 mM
2	Phosphate buffer			50 mM
3	NaCl			200 mM
4	DTT			5 mM
5	D2O			7 %

8 3D HN(CO)CA

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 300 K, pH 6.5, Details Phosphate buffer, pH=6.5 200 mM NaCl 5.0 mM DTT

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1 mM
2	Phosphate buffer			50 mM
3	NaCl			200 mM
4	DTT			5 mM
5	D2O			7 %

9 3D HCCH-TOCSY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 300 K, pH 6.5, Details Phosphate buffer, pH=6.5 200 mM NaCl 5.0 mM DTT

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1 mM
2	Phosphate buffer			50 mM
3	NaCl			200 mM
4	DTT			5 mM
5	D2O			7 %

10 3D HNHA

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 300 K, pH 6.5, Details Phosphate buffer, pH=6.5 200 mM NaCl 5.0 mM DTT

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1 mM
2	Phosphate buffer			50 mM
3	NaCl			200 mM
4	DTT			5 mM
5	D2O			7 %

11 3D 1H-15N NOESY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 300 K, pH 6.5, Details Phosphate buffer, pH=6.5 200 mM NaCl 5.0 mM DTT

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1 mM
2	Phosphate buffer			50 mM
3	NaCl			200 mM
4	DTT			5 mM
5	D2O			7 %

12 3D 1H-15N TOCSY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 300 K, pH 6.5, Details Phosphate buffer, pH=6.5 200 mM NaCl 5.0 mM DTT

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1 mM
2	Phosphate buffer			50 mM
3	NaCl			200 mM
4	DTT			5 mM
5	D2O			7 %

13 3D 1H-13C NOESY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 300 K, pH 6.5, Details Phosphate buffer, pH=6.5 200 mM NaCl 5.0 mM DTT

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1 mM
2	Phosphate buffer			50 mM
3	NaCl			200 mM
4	DTT			5 mM
5	D2O			7 %

14 3D HNHB

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 300 K, pH 6.5, Details Phosphate buffer, pH=6.5 200 mM NaCl 5.0 mM DTT

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1 mM
2	Phosphate buffer			50 mM
3	NaCl			200 mM
4	DTT			5 mM
5	D2O			7 %

15 3D HCCH-COSY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 300 K, pH 6.5, Details Phosphate buffer, pH=6.5 200 mM NaCl 5.0 mM DTT

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1 mM
2	Phosphate buffer			50 mM
3	NaCl			200 mM
4	DTT			5 mM
5	D2O			7 %

16 3D HCACO

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 300 K, pH 6.5, Details Phosphate buffer, pH=6.5 200 mM NaCl 5.0 mM DTT

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1 mM
2	Phosphate buffer			50 mM
3	NaCl			200 mM
4	DTT			5 mM
5	D2O			7 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15325_2jrb.nef
Input source #2: Coordindates	2jrb.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

----280-------290-------300-------310-------320-------330-------340-------350-------360-
MQVTYKGRPIRITPDFSPETMKARRAWTDVIQTLREHKCQPRLLYPAKLSITIDGETKVFHDKTKFTQYLSTNPALQRIITEKKQYKD
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MQVTYKGRPIRITPDFSPETMKARRAWTDVIQTLREHKCQPRLLYPAKLSITIDGETKVFHDKTKFTQYLSTNPALQRIITEKKQYKD
--------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	88	0	0	100.0

Content subtype: combined_15325_2jrb.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1031		100.0 (chain: A, length: 88)
1	Distance restraints	CNS/XPLOR_distance_constraints_6	Warning	1655 (1)	noe	98.9 (chain: A, length: 88)
2	Distance restraints	CNS/XPLOR_distance_constraints_5	OK	63 (1)	hbond	48.9 (chain: A, length: 88)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	134 (134)	.	94.3 (chain: A, length: 88)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 88, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 534
  - ¹³C chemical shifts: 413
  - ¹⁵N chemical shifts: 84
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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: CNS/XPLOR_distance_constraints_6
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 88, Sequence coverage: 98.9%
- Total number of restraints: 1653
- Weight of restraints: 1.0 (1653)
- Potential type of restraints: square-well-parabolic (1653)
- Range of distance target values: 2.25, 4.15 (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_5
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 88, Sequence coverage: 48.9%
  - Total number of restraints: 63
  - Weight of restraints: 1.0 (63)
  - Potential type of restraints: square-well-parabolic (63)
  - Range of distance target values: 1.9, 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_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 88, Sequence coverage: 94.3%
- Total number of restraints: 134
- Total number of restraints per polymer type: 134
- Weight of restraints: 1.0 (134)
- Potential type of restraints: square-well-parabolic (134)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords RNA binding domain