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BMRB: 18349

2LR6

NMR structure of a LINE-1 type transposase domain-containing protein 1 (L1TD1) from HOMO SAPINES

Authors

Serrano, P., Geralt, M., Mohanty, B., Wuthrich, K.

Assembly

RF2209A

Entity

1. RF2209A (polymer, Thiol state: all free), 176 monomers, 19780.60 Da Detail

GVLMDEGAVL TLAADLSSAT LDISKQWSNV FNILRENDFE PKFLCEVKLA FKCDGEIKTF SDLQSLRKFA SQKSSMKELL KDVLPQKEGV LMDEGAVLTL AADLSSATLD ISKQWSNVFN ILRENDFEPK FLCEVKLAFK CDGEIKTFSD LQSLRKFASQ KSSMKELLKD VLPQKE

Formula weight

19780.6 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 58.0 %, Completeness: 49.7 %, Completeness (bb): 48.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	49.7 % (1048 of 2108)	52.5 % (578 of 1100)	44.8 % (367 of 820)	54.8 % (103 of 188)
Backbone	48.7 % (510 of 1048)	54.2 % (192 of 354)	42.5 % (222 of 522)	55.8 % (96 of 172)
Sidechain	51.7 % (636 of 1230)	51.7 % (386 of 746)	51.9 % (243 of 468)	43.8 % (7 of 16)
Aromatic	43.1 % (62 of 144)	47.2 % (34 of 72)	38.6 % (27 of 70)	50.0 % (1 of 2)
Methyl	56.4 % (115 of 204)	57.8 % (59 of 102)	54.9 % (56 of 102)

1. L1TD1

GVLMDEGAVL TLAADLSSAT LDISKQWSNV FNILRENDFE PKFLCEVKLA FKCDGEIKTF SDLQSLRKFA SQKSSMKELL KDVLPQKEGV LMDEGAVLTL AADLSSATLD ISKQWSNVFN ILRENDFEPK FLCEVKLAFK CDGEIKTFSD LQSLRKFASQ KSSMKELLKD VLPQKE

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	L1TD1	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium azide	natural abundance		5 mM
3	sodium chloride	natural abundance		50 mM
4	sodium phosphate	natural abundance		25 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

LACS Plot; CA

Referencing offset: 0.0 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: 0.0 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: 0.01 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2LR6, Strand ID: A, B Detail

Release date

2012-07-01

Citation

NMR structure of a LINE-1 type transposase domain-containing protein 1 (L1TD1) from HOMO SAPINES
Serrano, P., Geralt, M., Mohanty, B., Wuthrich, K.
Not known

Related entities 1. RF2209A, : 19 entities Detail

Experiments performed 7 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	L1TD1	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium azide	natural abundance		5 mM
3	sodium chloride	natural abundance		50 mM
4	sodium phosphate	natural abundance		25 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

2 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	L1TD1	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium azide	natural abundance		5 mM
3	sodium chloride	natural abundance		50 mM
4	sodium phosphate	natural abundance		25 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

3 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	L1TD1	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium azide	natural abundance		5 mM
3	sodium chloride	natural abundance		50 mM
4	sodium phosphate	natural abundance		25 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

4 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	L1TD1	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium azide	natural abundance		5 mM
3	sodium chloride	natural abundance		50 mM
4	sodium phosphate	natural abundance		25 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

5 APSY 5D-HACACONH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	L1TD1	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium azide	natural abundance		5 mM
3	sodium chloride	natural abundance		50 mM
4	sodium phosphate	natural abundance		25 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

6 APSY 5D-CBCACONH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	L1TD1	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium azide	natural abundance		5 mM
3	sodium chloride	natural abundance		50 mM
4	sodium phosphate	natural abundance		25 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

7 ASPY 4D-HACANH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	L1TD1	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium azide	natural abundance		5 mM
3	sodium chloride	natural abundance		50 mM
4	sodium phosphate	natural abundance		25 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_18349_2lr6.nef
Input source #2: Coordindates	2lr6.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--------
GVLMDEGAVLTLAADLSSATLDISKQWSNVFNILRENDFEPKFLCEVKLAFKCDGEIKTFSDLQSLRKFASQKSSMKELLKDVLPQKE
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GVLMDEGAVLTLAADLSSATLDISKQWSNVFNILRENDFEPKFLCEVKLAFKCDGEIKTFSDLQSLRKFASQKSSMKELLKDVLPQKE

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

-------110-------120-------130-------140-------150-------160-------170-------180--------
GVLMDEGAVLTLAADLSSATLDISKQWSNVFNILRENDFEPKFLCEVKLAFKCDGEIKTFSDLQSLRKFASQKSSMKELLKDVLPQKE
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GVLMDEGAVLTLAADLSSATLDISKQWSNVFNILRENDFEPKFLCEVKLAFKCDGEIKTFSDLQSLRKFASQKSSMKELLKDVLPQKE
--------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
B	B	88	0	0	100.0

Content subtype: combined_18349_2lr6.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	892		97.7 (chain: A, length: 88)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	4388 (1)	noe	95.5 (chain: A, length: 88), 95.5 (chain: B, 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: 97.7%
- Total number of assignments
  - ¹H chemical shifts: 510
  - ¹³C chemical shifts: 294
  - ¹⁵N chemical shifts: 88
- 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: 88, Sequence coverage: 95.5%
  - Entity_assembly_ID: B, Chain length: 88, Sequence coverage: 95.5%
- Total number of restraints: 4382
- Weight of restraints: 1.0 (4382)
- Potential type of restraints: upper-bound-parabolic (4382)
- Range of distance target values: 2.36, 5.5 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map

Keywords JCSG, L1TD1