Identification and structural characterization of LytU
GSKWEDFFRG SRITETFGKY QHSPFDGKHY GIDFALPKGT PIKAPTNGKV TRIFNNELGG KVLQIAEDNG EYHQWYLHLD KYNVKVGDRV KAGDIIAYSG NTGIQTTGAH LHFQRMKGGV GNAYAEDPKP FIDQLPDGER SLYDL
ID | Type | Value order | Atom ID 1 | Atom ID 2 |
---|---|---|---|---|
1 | na | sing | 1:HIS29:NE2 | 2:ZN1:ZN |
2 | na | sing | 1:ASP33:OD1 | 2:ZN1:ZN |
3 | na | sing | 1:ASP33:OD2 | 2:ZN1:ZN |
4 | na | sing | 1:HIS112:ND1 | 2:ZN1:ZN |
Polymer type: polypeptide(L)
Total | 1H | 13C | 15N | |
---|---|---|---|---|
All | 87.1 % (1481 of 1701) | 94.8 % (841 of 887) | 75.9 % (502 of 661) | 90.2 % (138 of 153) |
Backbone | 82.5 % (706 of 856) | 94.4 % (285 of 302) | 70.7 % (294 of 416) | 92.0 % (127 of 138) |
Sidechain | 92.8 % (901 of 971) | 95.0 % (556 of 585) | 90.0 % (334 of 371) | 73.3 % (11 of 15) |
Aromatic | 78.1 % (150 of 192) | 94.8 % (91 of 96) | 60.6 % (57 of 94) | 100.0 % (2 of 2) |
Methyl | 100.0 % (128 of 128) | 100.0 % (64 of 64) | 100.0 % (64 of 64) |
1. entity 1
GSKWEDFFRG SRITETFGKY QHSPFDGKHY GIDFALPKGT PIKAPTNGKV TRIFNNELGG KVLQIAEDNG EYHQWYLHLD KYNVKVGDRV KAGDIIAYSG NTGIQTTGAH LHFQRMKGGV GNAYAEDPKP FIDQLPDGER SLYDLSolvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 308 K, pH 6.5, Details 0.5 mM [U-13C; U-15N] LytU, 20 mM bisTris buffer, 0.5 mM zinc chloride, 93% H2O/7% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Bis-Tris buffer | 20 mM | ||
2 | LytU | [U-13C; U-15N] | 0.5 mM |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl carbons | 46.01 ppm | internal | indirect | 0.2514495 |
1H | water | protons | 4.67 ppm | internal | direct | 1.0 |
15N | liquid anhydrous ammonia | nitrogen | 117.79 ppm | internal | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl carbons | 46.01 ppm | internal | indirect | 0.2514495 |
1H | water | protons | 4.67 ppm | internal | direct | 1.0 |
15N | liquid anhydrous ammonia | nitrogen | 117.79 ppm | internal | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl carbons | 46.01 ppm | internal | indirect | 0.2514495 |
1H | water | protons | 4.67 ppm | internal | direct | 1.0 |
15N | liquid anhydrous ammonia | nitrogen | 117.79 ppm | internal | indirect | 0.1013291 |
Varian INOVA - 800 MHz
State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 308 K, pH 6.5, Details 0.5 mM [U-13C; U-15N] LytU, 20 mM bisTris buffer, 0.5 mM zinc chloride, 93% H2O/7% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Bis-Tris buffer | 20 mM | ||
2 | LytU | [U-13C; U-15N] | 0.5 mM |
Varian INOVA - 800 MHz
State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 308 K, pH 6.5, Details 0.5 mM [U-13C; U-15N] LytU, 20 mM bisTris buffer, 0.5 mM zinc chloride, 93% H2O/7% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Bis-Tris buffer | 20 mM | ||
2 | LytU | [U-13C; U-15N] | 0.5 mM |
Varian INOVA - 800 MHz
State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 308 K, pH 6.5, Details 0.5 mM [U-13C; U-15N] LytU, 20 mM bisTris buffer, 0.5 mM zinc chloride, 93% H2O/7% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Bis-Tris buffer | 20 mM | ||
2 | LytU | [U-13C; U-15N] | 0.5 mM |
Varian INOVA - 800 MHz
State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 308 K, pH 6.5, Details 0.5 mM [U-13C; U-15N] LytU, 20 mM bisTris buffer, 0.5 mM zinc chloride, 93% H2O/7% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Bis-Tris buffer | 20 mM | ||
2 | LytU | [U-13C; U-15N] | 0.5 mM |
Varian INOVA - 800 MHz
State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 308 K, pH 6.5, Details 0.5 mM [U-13C; U-15N] LytU, 20 mM bisTris buffer, 0.5 mM zinc chloride, 93% H2O/7% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Bis-Tris buffer | 20 mM | ||
2 | LytU | [U-13C; U-15N] | 0.5 mM |
Varian INOVA - 800 MHz
State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 308 K, pH 6.5, Details 0.5 mM [U-13C; U-15N] LytU, 20 mM bisTris buffer, 0.5 mM zinc chloride, 93% H2O/7% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Bis-Tris buffer | 20 mM | ||
2 | LytU | [U-13C; U-15N] | 0.5 mM |
Varian INOVA - 800 MHz
State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 308 K, pH 6.5, Details 0.5 mM [U-13C; U-15N] LytU, 20 mM bisTris buffer, 0.5 mM zinc chloride, 93% H2O/7% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Bis-Tris buffer | 20 mM | ||
2 | LytU | [U-13C; U-15N] | 0.5 mM |
Varian INOVA - 800 MHz
State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 308 K, pH 6.5, Details 0.5 mM [U-13C; U-15N] LytU, 20 mM bisTris buffer, 0.5 mM zinc chloride, 93% H2O/7% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Bis-Tris buffer | 20 mM | ||
2 | LytU | [U-13C; U-15N] | 0.5 mM |
Varian INOVA - 800 MHz
State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 308 K, pH 6.5, Details 0.5 mM [U-13C; U-15N] LytU, 20 mM bisTris buffer, 0.5 mM zinc chloride, 93% H2O/7% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Bis-Tris buffer | 20 mM | ||
2 | LytU | [U-13C; U-15N] | 0.5 mM |
Varian INOVA - 800 MHz
State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 308 K, pH 6.5, Details 0.5 mM [U-13C; U-15N] LytU, 20 mM bisTris buffer, 0.5 mM zinc chloride, 93% H2O/7% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Bis-Tris buffer | 20 mM | ||
2 | LytU | [U-13C; U-15N] | 0.5 mM |
Varian INOVA - 800 MHz
State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 308 K, pH 6.5, Details 0.5 mM [U-13C; U-15N] LytU, 20 mM bisTris buffer, 0.5 mM zinc chloride, 93% H2O/7% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Bis-Tris buffer | 20 mM | ||
2 | LytU | [U-13C; U-15N] | 0.5 mM |
Varian INOVA - 800 MHz
State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 308 K, pH 6.5, Details 0.5 mM [U-13C; U-15N] LytU, 20 mM bisTris buffer, 0.5 mM zinc chloride, 93% H2O/7% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Bis-Tris buffer | 20 mM | ||
2 | LytU | [U-13C; U-15N] | 0.5 mM |
Varian INOVA - 800 MHz
State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 308 K, pH 6.5, Details 0.5 mM [U-13C; U-15N] LytU, 20 mM bisTris buffer, 0.5 mM zinc chloride, 93% H2O/7% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Bis-Tris buffer | 20 mM | ||
2 | LytU | [U-13C; U-15N] | 0.5 mM |
Varian INOVA - 800 MHz
State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 308 K, pH 6.5, Details 0.5 mM [U-13C; U-15N] LytU, 20 mM bisTris buffer, 0.5 mM zinc chloride, 93% H2O/7% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Bis-Tris buffer | 20 mM | ||
2 | LytU | [U-13C; U-15N] | 0.5 mM |
Varian INOVA - 800 MHz
State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 308 K, pH 6.5, Details 0.5 mM [U-13C; U-15N] LytU, 20 mM bisTris buffer, 0.5 mM zinc chloride, 93% H2O/7% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Bis-Tris buffer | 20 mM | ||
2 | LytU | [U-13C; U-15N] | 0.5 mM |
Properties
Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints | combined_30130_5kqb.nef |
Input source #2: Coordindates | 5kqb.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 | True (see coodinates for details) |
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)
Ptnr_site_1 | Ptnr_site_2 | Redox_state_prediction_1 | Redox_state_prediction_2 | Distance (Ã…) |
---|---|---|---|---|
1:29:HIS:NE2 | 2:1:ZN:ZN | unknown | unknown | n/a |
1:33:ASP:OD1 | 2:1:ZN:ZN | unknown | unknown | n/a |
1:33:ASP:OD2 | 2:1:ZN:ZN | unknown | unknown | n/a |
1:112:HIS:ND1 | 2:1:ZN:ZN | unknown | unknown | n/a |
Non-standard residues
Chain_ID | Seq_ID | Comp_ID | Chem_comp_name | Experimental evidences |
---|---|---|---|---|
B | 1 | ZN | ZINC ION | None |
Sequence alignments
--50-------60--------70--------80--------90-------100-------110-------120-------130-------140------- GSKWEDFFRGSRITETFGKYQHSPFDGKHYGIDFALPKGTPIKAPTNGKVTRIFNNELGGKVLQIAEDNGEYHQWYLHLDKYNVKVGDRVKAGDIIAYSG |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| GSKWEDFFRGSRITETFGKYQHSPFDGKHYGIDFALPKGTPIKAPTNGKVTRIFNNELGGKVLQIAEDNGEYHQWYLHLDKYNVKVGDRVKAGDIIAYSG --------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 150-------160-------170-------180-------190-- NTGIQTTGAHLHFQRMKGGVGNAYAEDPKPFIDQLPDGERSLYDL ||||||||||||||||||||||||||||||||||||||||||||| NTGIQTTGAHLHFQRMKGGVGNAYAEDPKPFIDQLPDGERSLYDL -------110-------120-------130-------140-----
Chain assignments
Entity_assembly_ID (NMR) | Auth_asym_ID (model) | Length | Unmapped | Conflict | Sequence coverage (%) |
---|---|---|---|---|---|
A | A | 145 | 0 | 0 | 100.0 |
Content subtype: combined_30130_5kqb.nef
Assigned chemical shifts
--50-------60--------70--------80--------90-------100-------110-------120-------130-------140------- GSKWEDFFRGSRITETFGKYQHSPFDGKHYGIDFALPKGTPIKAPTNGKVTRIFNNELGGKVLQIAEDNGEYHQWYLHLDKYNVKVGDRVKAGDIIAYSG ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| .SKWEDFFRGSRITETFGKYQHSPFDGKHYGIDFALPKGTPIKAPTNGKVTRIFNNELGGKVLQIAEDNGEYHQWYLHLDKYNVKVGDRVKAGDIIAYSG 150-------160-------170-------180-------190-- NTGIQTTGAHLHFQRMKGGVGNAYAEDPKPFIDQLPDGERSLYDL ||||||||||||||||||||||||||||||||||||||||||||| NTGIQTTGAHLHFQRMKGGVGNAYAEDPKPFIDQLPDGERSLYDL
Comp_index_ID | Comp_ID | Atom_ID | CS value (ppm) |
---|---|---|---|
87 | THR | HG1 | 6.192 |
98 | THR | HG1 | 5.643 |
120 | HIS | HE2 | 11.091 |
120 | HIS | NE2 | 163.423 |
157 | HIS | HD1 | 12.304 |
159 | HIS | HE2 | 12.958 |
159 | HIS | NE2 | 167.713 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 887 | 846 | 95.4 |
13C chemical shifts | 661 | 474 | 71.7 |
15N chemical shifts | 159 | 136 | 85.5 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 302 | 285 | 94.4 |
13C chemical shifts | 290 | 143 | 49.3 |
15N chemical shifts | 138 | 124 | 89.9 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 585 | 561 | 95.9 |
13C chemical shifts | 371 | 331 | 89.2 |
15N chemical shifts | 21 | 12 | 57.1 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 65 | 65 | 100.0 |
13C chemical shifts | 65 | 65 | 100.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 96 | 91 | 94.8 |
13C chemical shifts | 94 | 55 | 58.5 |
15N chemical shifts | 2 | 2 | 100.0 |
Covalent bonds
Distance restraints
--50-------60--------70--------80--------90-------100-------110-------120-------130-------140------- GSKWEDFFRGSRITETFGKYQHSPFDGKHYGIDFALPKGTPIKAPTNGKVTRIFNNELGGKVLQIAEDNGEYHQWYLHLDKYNVKVGDRVKAGDIIAYSG ||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ..KWEDFFR.SRITETFGKYQHSPFDGKHYGIDFALPKGTPIKAPTNGKVTRIFNNELGGKVLQIAEDNGEYHQWYLHLDKYNVKVGDRVKAGDIIAYSG 150-------160-------170-------180-------190-- NTGIQTTGAHLHFQRMKGGVGNAYAEDPKPFIDQLPDGERSLYDL || |||| ||||||||||||||||||||||||||||||||||||| NT.IQTT.AHLHFQRMKGGVGNAYAEDPKPFIDQLPDGERSLYDL