NMR structure of a LINE-1 type transposase domain-containing protein 1 (L1TD1) from HOMO SAPINES
GVLMDEGAVL TLAADLSSAT LDISKQWSNV FNILRENDFE PKFLCEVKLA FKCDGEIKTF SDLQSLRKFA SQKSSMKELL KDVLPQKEGV LMDEGAVLTL AADLSSATLD ISKQWSNVFN ILRENDFEPK FLCEVKLAFK CDGEIKTFSD LQSLRKFASQ KSSMKELLKD VLPQKE
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 VLPQKESolvent 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 % |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | na | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | na | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | na | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | na | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | na | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | na | indirect | 0.1013291 |
Bruker Avance - 600 MHz
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 % |
Bruker Avance - 800 MHz
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 % |
Bruker Avance - 800 MHz
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 % |
Bruker Avance - 800 MHz
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 % |
Bruker Avance - 600 MHz
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 % |
Bruker Avance - 600 MHz
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 % |
Bruker Avance - 600 MHz
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 % |
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
NoneOther bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)
NoneNon-standard residues
NoneSequence alignments
--------10--------20--------30--------40--------50--------60--------70--------80-------- GVLMDEGAVLTLAADLSSATLDISKQWSNVFNILRENDFEPKFLCEVKLAFKCDGEIKTFSDLQSLRKFASQKSSMKELLKDVLPQKE |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| GVLMDEGAVLTLAADLSSATLDISKQWSNVFNILRENDFEPKFLCEVKLAFKCDGEIKTFSDLQSLRKFASQKSSMKELLKDVLPQKE
-------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
Assigned chemical shifts
--------10--------20--------30--------40--------50--------60--------70--------80-------- GVLMDEGAVLTLAADLSSATLDISKQWSNVFNILRENDFEPKFLCEVKLAFKCDGEIKTFSDLQSLRKFASQKSSMKELLKDVLPQKE |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ..LMDEGAVLTLAADLSSATLDISKQWSNVFNILRENDFEPKFLCEVKLAFKCDGEIKTFSDLQSLRKFASQKSSMKELLKDVLPQKE
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 550 | 510 | 92.7 |
13C chemical shifts | 410 | 294 | 71.7 |
15N chemical shifts | 96 | 88 | 91.7 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 177 | 165 | 93.2 |
13C chemical shifts | 176 | 86 | 48.9 |
15N chemical shifts | 86 | 79 | 91.9 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 373 | 345 | 92.5 |
13C chemical shifts | 234 | 208 | 88.9 |
15N chemical shifts | 10 | 9 | 90.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 53 | 49 | 92.5 |
13C chemical shifts | 53 | 48 | 90.6 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 36 | 29 | 80.6 |
13C chemical shifts | 35 | 22 | 62.9 |
15N chemical shifts | 1 | 1 | 100.0 |
Distance restraints
--------10--------20--------30--------40--------50--------60--------70--------80-------- GVLMDEGAVLTLAADLSSATLDISKQWSNVFNILRENDFEPKFLCEVKLAFKCDGEIKTFSDLQSLRKFASQKSSMKELLKDVLPQKE ||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||| |||||||||||||| ..LMDEGAVLTLAADLSSATLDISKQWSN.FNILRENDFEPKFLCEVKLAFKCDGEIKTFSDLQSLRKFASQK.SMKELLKDVLPQKE
-------110-------120-------130-------140-------150-------160-------170-------180-------- GVLMDEGAVLTLAADLSSATLDISKQWSNVFNILRENDFEPKFLCEVKLAFKCDGEIKTFSDLQSLRKFASQKSSMKELLKDVLPQKE ||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||| |||||||||||||| ..LMDEGAVLTLAADLSSATLDISKQWSN.FNILRENDFEPKFLCEVKLAFKCDGEIKTFSDLQSLRKFASQK.SMKELLKDVLPQKE