Solution structure of the zinc finger AFV1p06 protein from the hyperthermophilic archaeal virus AFV1
Polymer type: polypeptide(L)
Total | 1H | 13C | 15N | |
---|---|---|---|---|
All | 92.7 % (682 of 736) | 90.9 % (350 of 385) | 94.8 % (272 of 287) | 93.8 % (60 of 64) |
Backbone | 94.3 % (332 of 352) | 93.2 % (110 of 118) | 94.9 % (167 of 176) | 94.8 % (55 of 58) |
Sidechain | 91.9 % (406 of 442) | 89.9 % (240 of 267) | 95.3 % (161 of 169) | 83.3 % (5 of 6) |
Aromatic | 92.9 % (52 of 56) | 92.9 % (26 of 28) | 92.9 % (26 of 28) | |
Methyl | 97.3 % (72 of 74) | 94.6 % (35 of 37) | 100.0 % (37 of 37) |
1. AFV1p06
MIEVSSMERV YQCLRCGLTF RTKKQLIRHL VNTEKVNPLS IDYYYQSFSV SLKDVNKIISolvent system 88% H2O/12% D2O, Pressure 1 atm, Temperature 298.15 (±0.1) K, pH 7.4, Details 50 mM Na-HEPES 150 mM NaCl 50uM ZnCl2 3 mM DTT 12% D2O pH 7.4
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | AFV1p06 | [U-98% 13C; U-98% 15N] | 0.8-1 mM | |
2 | Na-HEPES | natural abundance | 50 mM | |
3 | NaCl | natural abundance | 150 mM | |
4 | ZnCl2 | natural abundance | 50 uM | |
5 | DTT | natural abundance | 3 mM |
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 |
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 |
Varian NMR System - 600 MHz
State isotropic, Solvent system 88% H2O/12% D2O, Pressure 1 atm, Temperature 298.15 (±0.1) K, pH 7.4, Details 50 mM Na-HEPES 150 mM NaCl 50uM ZnCl2 3 mM DTT 12% D2O pH 7.4
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | AFV1p06 | [U-98% 13C; U-98% 15N] | 0.8-1 mM | |
2 | Na-HEPES | natural abundance | 50 mM | |
3 | NaCl | natural abundance | 150 mM | |
4 | ZnCl2 | natural abundance | 50 uM | |
5 | DTT | natural abundance | 3 mM |
Varian NMR System - 600 MHz
State isotropic, Solvent system 88% H2O/12% D2O, Pressure 1 atm, Temperature 298.15 (±0.1) K, pH 7.4, Details 50 mM Na-HEPES 150 mM NaCl 50uM ZnCl2 3 mM DTT 12% D2O pH 7.4
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | AFV1p06 | [U-98% 13C; U-98% 15N] | 0.8-1 mM | |
2 | Na-HEPES | natural abundance | 50 mM | |
3 | NaCl | natural abundance | 150 mM | |
4 | ZnCl2 | natural abundance | 50 uM | |
5 | DTT | natural abundance | 3 mM |
Varian NMR System - 600 MHz
State isotropic, Solvent system 88% H2O/12% D2O, Pressure 1 atm, Temperature 298.15 (±0.1) K, pH 7.4, Details 50 mM Na-HEPES 150 mM NaCl 50uM ZnCl2 3 mM DTT 12% D2O pH 7.4
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | AFV1p06 | [U-98% 13C; U-98% 15N] | 0.8-1 mM | |
2 | Na-HEPES | natural abundance | 50 mM | |
3 | NaCl | natural abundance | 150 mM | |
4 | ZnCl2 | natural abundance | 50 uM | |
5 | DTT | natural abundance | 3 mM |
Varian NMR System - 600 MHz
State isotropic, Solvent system 88% H2O/12% D2O, Pressure 1 atm, Temperature 298.15 (±0.1) K, pH 7.4, Details 50 mM Na-HEPES 150 mM NaCl 50uM ZnCl2 3 mM DTT 12% D2O pH 7.4
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | AFV1p06 | [U-98% 13C; U-98% 15N] | 0.8-1 mM | |
2 | Na-HEPES | natural abundance | 50 mM | |
3 | NaCl | natural abundance | 150 mM | |
4 | ZnCl2 | natural abundance | 50 uM | |
5 | DTT | natural abundance | 3 mM |
Varian NMR System - 600 MHz
State isotropic, Solvent system 88% H2O/12% D2O, Pressure 1 atm, Temperature 298.15 (±0.1) K, pH 7.4, Details 50 mM Na-HEPES 150 mM NaCl 50uM ZnCl2 3 mM DTT 12% D2O pH 7.4
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | AFV1p06 | [U-98% 13C; U-98% 15N] | 0.8-1 mM | |
2 | Na-HEPES | natural abundance | 50 mM | |
3 | NaCl | natural abundance | 150 mM | |
4 | ZnCl2 | natural abundance | 50 uM | |
5 | DTT | natural abundance | 3 mM |
Varian NMR System - 600 MHz
State isotropic, Solvent system 88% H2O/12% D2O, Pressure 1 atm, Temperature 298.15 (±0.1) K, pH 7.4, Details 50 mM Na-HEPES 150 mM NaCl 50uM ZnCl2 3 mM DTT 12% D2O pH 7.4
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | AFV1p06 | [U-98% 13C; U-98% 15N] | 0.8-1 mM | |
2 | Na-HEPES | natural abundance | 50 mM | |
3 | NaCl | natural abundance | 150 mM | |
4 | ZnCl2 | natural abundance | 50 uM | |
5 | DTT | natural abundance | 3 mM |
Varian NMR System - 600 MHz
State isotropic, Solvent system 88% H2O/12% D2O, Pressure 1 atm, Temperature 298.15 (±0.1) K, pH 7.4, Details 50 mM Na-HEPES 150 mM NaCl 50uM ZnCl2 3 mM DTT 12% D2O pH 7.4
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | AFV1p06 | [U-98% 13C; U-98% 15N] | 0.8-1 mM | |
2 | Na-HEPES | natural abundance | 50 mM | |
3 | NaCl | natural abundance | 150 mM | |
4 | ZnCl2 | natural abundance | 50 uM | |
5 | DTT | natural abundance | 3 mM |
Varian NMR System - 600 MHz
State isotropic, Solvent system 88% H2O/12% D2O, Pressure 1 atm, Temperature 298.15 (±0.1) K, pH 7.4, Details 50 mM Na-HEPES 150 mM NaCl 50uM ZnCl2 3 mM DTT 12% D2O pH 7.4
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | AFV1p06 | [U-98% 13C; U-98% 15N] | 0.8-1 mM | |
2 | Na-HEPES | natural abundance | 50 mM | |
3 | NaCl | natural abundance | 150 mM | |
4 | ZnCl2 | natural abundance | 50 uM | |
5 | DTT | natural abundance | 3 mM |
Varian NMR System - 600 MHz
State isotropic, Solvent system 88% H2O/12% D2O, Pressure 1 atm, Temperature 298.15 (±0.1) K, pH 7.4, Details 50 mM Na-HEPES 150 mM NaCl 50uM ZnCl2 3 mM DTT 12% D2O pH 7.4
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | AFV1p06 | [U-98% 13C; U-98% 15N] | 0.8-1 mM | |
2 | Na-HEPES | natural abundance | 50 mM | |
3 | NaCl | natural abundance | 150 mM | |
4 | ZnCl2 | natural abundance | 50 uM | |
5 | DTT | natural abundance | 3 mM |
Varian NMR System - 600 MHz
State isotropic, Solvent system 88% H2O/12% D2O, Pressure 1 atm, Temperature 298.15 (±0.1) K, pH 7.4, Details 50 mM Na-HEPES 150 mM NaCl 50uM ZnCl2 3 mM DTT 12% D2O pH 7.4
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | AFV1p06 | [U-98% 13C; U-98% 15N] | 0.8-1 mM | |
2 | Na-HEPES | natural abundance | 50 mM | |
3 | NaCl | natural abundance | 150 mM | |
4 | ZnCl2 | natural abundance | 50 uM | |
5 | DTT | natural abundance | 3 mM |
Varian NMR System - 600 MHz
State isotropic, Solvent system 88% H2O/12% D2O, Pressure 1 atm, Temperature 298.15 (±0.1) K, pH 7.4, Details 50 mM Na-HEPES 150 mM NaCl 50uM ZnCl2 3 mM DTT 12% D2O pH 7.4
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | AFV1p06 | [U-98% 13C; U-98% 15N] | 0.8-1 mM | |
2 | Na-HEPES | natural abundance | 50 mM | |
3 | NaCl | natural abundance | 150 mM | |
4 | ZnCl2 | natural abundance | 50 uM | |
5 | DTT | natural abundance | 3 mM |
Varian NMR System - 600 MHz
State isotropic, Solvent system 88% H2O/12% D2O, Pressure 1 atm, Temperature 298.15 (±0.1) K, pH 7.4, Details 50 mM Na-HEPES 150 mM NaCl 50uM ZnCl2 3 mM DTT 12% D2O pH 7.4
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | AFV1p06 | [U-98% 13C; U-98% 15N] | 0.8-1 mM | |
2 | Na-HEPES | natural abundance | 50 mM | |
3 | NaCl | natural abundance | 150 mM | |
4 | ZnCl2 | natural abundance | 50 uM | |
5 | DTT | natural abundance | 3 mM |
Varian NMR System - 600 MHz
State isotropic, Solvent system 88% H2O/12% D2O, Pressure 1 atm, Temperature 298.15 (±0.1) K, pH 7.4, Details 50 mM Na-HEPES 150 mM NaCl 50uM ZnCl2 3 mM DTT 12% D2O pH 7.4
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | AFV1p06 | [U-98% 13C; U-98% 15N] | 0.8-1 mM | |
2 | Na-HEPES | natural abundance | 50 mM | |
3 | NaCl | natural abundance | 150 mM | |
4 | ZnCl2 | natural abundance | 50 uM | |
5 | DTT | natural abundance | 3 mM |
Varian NMR System - 600 MHz
State isotropic, Solvent system 88% H2O/12% D2O, Pressure 1 atm, Temperature 298.15 (±0.1) K, pH 7.4, Details 50 mM Na-HEPES 150 mM NaCl 50uM ZnCl2 3 mM DTT 12% D2O pH 7.4
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | AFV1p06 | [U-98% 13C; U-98% 15N] | 0.8-1 mM | |
2 | Na-HEPES | natural abundance | 50 mM | |
3 | NaCl | natural abundance | 150 mM | |
4 | ZnCl2 | natural abundance | 50 uM | |
5 | DTT | natural abundance | 3 mM |
Varian NMR System - 600 MHz
State isotropic, Solvent system 88% H2O/12% D2O, Pressure 1 atm, Temperature 298.15 (±0.1) K, pH 7.4, Details 50 mM Na-HEPES 150 mM NaCl 50uM ZnCl2 3 mM DTT 12% D2O pH 7.4
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | AFV1p06 | [U-98% 13C; U-98% 15N] | 0.8-1 mM | |
2 | Na-HEPES | natural abundance | 50 mM | |
3 | NaCl | natural abundance | 150 mM | |
4 | ZnCl2 | natural abundance | 50 uM | |
5 | DTT | natural abundance | 3 mM |
Varian NMR System - 600 MHz
State isotropic, Solvent system 88% H2O/12% D2O, Pressure 1 atm, Temperature 298.15 (±0.1) K, pH 7.4, Details 50 mM Na-HEPES 150 mM NaCl 50uM ZnCl2 3 mM DTT 12% D2O pH 7.4
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | AFV1p06 | [U-98% 13C; U-98% 15N] | 0.8-1 mM | |
2 | Na-HEPES | natural abundance | 50 mM | |
3 | NaCl | natural abundance | 150 mM | |
4 | ZnCl2 | natural abundance | 50 uM | |
5 | DTT | natural abundance | 3 mM |
Properties
Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints | combined_18570_2lvh.nef |
Input source #2: Coordindates | 2lvh.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 (Å) |
---|---|---|---|---|
1:34:GLU:OE2 | 2:1:ZN:ZN | unknown | unknown | n/a |
1:29:HIS:NE2 | 2:1:ZN:ZN | unknown | unknown | n/a |
1:16:CYS:SG | 2:1:ZN:ZN | unknown | unknown | n/a |
1:13:CYS:SG | 2:1:ZN:ZN | unknown | unknown | n/a |
1:34:GLU:OE1 | 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
--------10--------20--------30--------40--------50--------- MIEVSSMERVYQCLRCGLTFRTKKQLIRHLVNTEKVNPLSIDYYYQSFSVSLKDVNKII ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| MIEVSSMERVYQCLRCGLTFRTKKQLIRHLVNTEKVNPLSIDYYYQSFSVSLKDVNKII
Chain assignments
Entity_assembly_ID (NMR) | Auth_asym_ID (model) | Length | Unmapped | Conflict | Sequence coverage (%) |
---|---|---|---|---|---|
A | A | 59 | 0 | 0 | 100.0 |
Content subtype: combined_18570_2lvh.nef
Assigned chemical shifts
--------10--------20--------30--------40--------50--------- MIEVSSMERVYQCLRCGLTFRTKKQLIRHLVNTEKVNPLSIDYYYQSFSVSLKDVNKII ||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||| MIEVS.MERVYQCLRCGLTFRTKKQLIRHLVNTEKVNPLSIDYYYQSFSVSLKDVNKII
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 385 | 356 | 92.5 |
13C chemical shifts | 287 | 271 | 94.4 |
15N chemical shifts | 68 | 59 | 86.8 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 118 | 112 | 94.9 |
13C chemical shifts | 118 | 111 | 94.1 |
15N chemical shifts | 58 | 54 | 93.1 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 267 | 244 | 91.4 |
13C chemical shifts | 169 | 160 | 94.7 |
15N chemical shifts | 10 | 5 | 50.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 39 | 39 | 100.0 |
13C chemical shifts | 39 | 39 | 100.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 28 | 26 | 92.9 |
13C chemical shifts | 28 | 26 | 92.9 |
Covalent bonds
Distance restraints
--------10--------20--------30--------40--------50--------- MIEVSSMERVYQCLRCGLTFRTKKQLIRHLVNTEKVNPLSIDYYYQSFSVSLKDVNKII ||||||||||||||||||||||||||||||||||||||||||||| ......MERVYQCLRCGLTFRTKKQLIRHLVNTEKVNPLSIDYYYQSFSVS --------10--------20--------30--------40--------50-
--------10--------20--------30--------40--------50--------- MIEVSSMERVYQCLRCGLTFRTKKQLIRHLVNTEKVNPLSIDYYYQSFSVSLKDVNKII ||||||||||||||||||||||||||||||||||||||| | ........RVYQCLRCGLTFRTKKQLIRHLVNTEKVNPLSIDYYYQS..V --------10--------20--------30--------40--------50
Dihedral angle restraints
--------10--------20--------30--------40--------50--------- MIEVSSMERVYQCLRCGLTFRTKKQLIRHLVNTEKVNPLSIDYYYQSFSVSLKDVNKII ||||||||||||||||||||||||||||||||||||||||||||| ......MERVYQCLRCGLTFRTKKQLIRHLVNTEKVNPLSIDYYYQSFSVS --------10--------20--------30--------40--------50-