Impact of IR active probes on PDZ3 and its ligand binding studied by NMR and X-ray crystallography
FLGEEDIPRE PRRIVIHRGS TGLGFNIIGG EDGEGIFISF XLAGGPADLS GELRKGDQIL SVNGVDLRNA SHEQAAIALK NAGQTVTIIA QYKPEEYSRF EA
Polymer type: polypeptide(L)
Total | 1H | 13C | 15N | |
---|---|---|---|---|
All | 82.2 % (931 of 1132) | 87.1 % (512 of 588) | 74.3 % (326 of 439) | 88.6 % (93 of 105) |
Backbone | 93.6 % (560 of 598) | 96.2 % (204 of 212) | 91.3 % (264 of 289) | 94.8 % (92 of 97) |
Sidechain | 72.9 % (453 of 621) | 81.9 % (308 of 376) | 60.8 % (144 of 237) | 12.5 % (1 of 8) |
Aromatic | 29.7 % (22 of 74) | 51.4 % (19 of 37) | 8.1 % (3 of 37) | |
Methyl | 75.9 % (88 of 116) | 89.7 % (52 of 58) | 62.1 % (36 of 58) |
1. entity 1
FLGEEDIPRE PRRIVIHRGS TGLGFNIIGG EDGEGIFISF XLAGGPADLS GELRKGDQIL SVNGVDLRNA SHEQAAIALK NAGQTVTIIA QYKPEEYSRF EASolvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 0.5 mM [U-98% 13C; U-98% 15N] PDZ3, 50 mM sodium phosphate, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | PDZ3 | [U-98% 13C; U-98% 15N] | 0.5 mM | |
2 | sodium phosphate | natural abundance | 50 mM |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | internal | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | internal | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | internal | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | internal | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | internal | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | internal | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | internal | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | internal | indirect | 0.1013291 |
Bruker Avance III HD - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 0.5 mM [U-98% 13C; U-98% 15N] PDZ3, 50 mM sodium phosphate, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | PDZ3 | [U-98% 13C; U-98% 15N] | 0.5 mM | |
2 | sodium phosphate | natural abundance | 50 mM |
Bruker Avance III HD - 700 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 0.5 mM [U-98% 13C; U-98% 15N] PDZ3, 50 mM sodium phosphate, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | PDZ3 | [U-98% 13C; U-98% 15N] | 0.5 mM | |
2 | sodium phosphate | natural abundance | 50 mM |
Bruker Avance III HD - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 0.5 mM [U-98% 13C; U-98% 15N] PDZ3, 50 mM sodium phosphate, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | PDZ3 | [U-98% 13C; U-98% 15N] | 0.5 mM | |
2 | sodium phosphate | natural abundance | 50 mM |
Bruker DRX - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 0.5 mM [U-98% 13C; U-98% 15N] PDZ3, 50 mM sodium phosphate, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | PDZ3 | [U-98% 13C; U-98% 15N] | 0.5 mM | |
2 | sodium phosphate | natural abundance | 50 mM |
Bruker Avance III HD - 700 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 0.5 mM [U-98% 13C; U-98% 15N] PDZ3, 50 mM sodium phosphate, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | PDZ3 | [U-98% 13C; U-98% 15N] | 0.5 mM | |
2 | sodium phosphate | natural abundance | 50 mM |
Bruker Avance III HD - 700 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 0.5 mM [U-98% 13C; U-98% 15N] PDZ3, 50 mM sodium phosphate, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | PDZ3 | [U-98% 13C; U-98% 15N] | 0.5 mM | |
2 | sodium phosphate | natural abundance | 50 mM |
Bruker Avance III HD - 700 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 0.5 mM [U-98% 13C; U-98% 15N] PDZ3, 50 mM sodium phosphate, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | PDZ3 | [U-98% 13C; U-98% 15N] | 0.5 mM | |
2 | sodium phosphate | natural abundance | 50 mM |
Bruker Avance III HD - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 0.5 mM [U-98% 13C; U-98% 15N] PDZ3, 50 mM sodium phosphate, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | PDZ3 | [U-98% 13C; U-98% 15N] | 0.5 mM | |
2 | sodium phosphate | natural abundance | 50 mM |
Bruker Avance III HD - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 0.5 mM [U-98% 13C; U-98% 15N] PDZ3, 50 mM sodium phosphate, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | PDZ3 | [U-98% 13C; U-98% 15N] | 0.5 mM | |
2 | sodium phosphate | natural abundance | 50 mM |
Bruker Avance III HD - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 0.5 mM [U-98% 13C; U-98% 15N] PDZ3, 50 mM sodium phosphate, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | PDZ3 | [U-98% 13C; U-98% 15N] | 0.5 mM | |
2 | sodium phosphate | natural abundance | 50 mM |
Bruker Avance III HD - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 0.5 mM [U-98% 13C; U-98% 15N] PDZ3, 50 mM sodium phosphate, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | PDZ3 | [U-98% 13C; U-98% 15N] | 0.5 mM | |
2 | sodium phosphate | natural abundance | 50 mM |
Properties
Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints | combined_30307_5w72.nef |
Input source #2: Coordindates | 5w72.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…) |
---|---|---|---|---|
1:40:PHE:C | 1:41:AZH:N | unknown | unknown | n/a |
1:41:AZH:C | 1:42:LEU:N | unknown | unknown | n/a |
Non-standard residues
Chain_ID | Seq_ID | Comp_ID | Chem_comp_name | Experimental evidences |
---|---|---|---|---|
A | 341 | AZH | AZIDOHOMOALANINE | Assigned chemical shifts, Coordinates |
Sequence alignments
-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400 FLGEEDIPREPRRIVIHRGSTGLGFNIIGGEDGEGIFISFXLAGGPADLSGELRKGDQILSVNGVDLRNASHEQAAIALKNAGQTVTIIAQYKPEEYSRF |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| FLGEEDIPREPRRIVIHRGSTGLGFNIIGGEDGEGIFISFXLAGGPADLSGELRKGDQILSVNGVDLRNASHEQAAIALKNAGQTVTIIAQYKPEEYSRF --------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 -- EA || EA --
Chain assignments
Entity_assembly_ID (NMR) | Auth_asym_ID (model) | Length | Unmapped | Conflict | Sequence coverage (%) |
---|---|---|---|---|---|
A | A | 102 | 0 | 0 | 100.0 |
Content subtype: combined_30307_5w72.nef
Assigned chemical shifts
-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400 FLGEEDIPREPRRIVIHRGSTGLGFNIIGGEDGEGIFISFXLAGGPADLSGELRKGDQILSVNGVDLRNASHEQAAIALKNAGQTVTIIAQYKPEEYSRF ||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ..GEEDIPREPRRIVIHRG.TGLGFNIIGGEDGEGIFISFXLAGGPADLSGELRKGDQILSVNGVDLRNASHEQAAIALKNAGQTVTIIAQYKPEEYSRF -- EA || EA
Comp_index_ID | Comp_ID |
---|---|
341 | AZH |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 588 | 504 | 85.7 |
13C chemical shifts | 439 | 313 | 71.3 |
15N chemical shifts | 112 | 91 | 81.2 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 212 | 203 | 95.8 |
13C chemical shifts | 202 | 180 | 89.1 |
15N chemical shifts | 97 | 91 | 93.8 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 376 | 301 | 80.1 |
13C chemical shifts | 237 | 133 | 56.1 |
15N chemical shifts | 15 | 0 | 0.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 58 | 52 | 89.7 |
13C chemical shifts | 58 | 32 | 55.2 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 37 | 19 | 51.4 |
13C chemical shifts | 37 | 3 | 8.1 |
Covalent bonds
Distance restraints
-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400 FLGEEDIPREPRRIVIHRGSTGLGFNIIGGEDGEGIFISFXLAGGPADLSGELRKGDQILSVNGVDLRNASHEQAAIALKNAGQTVTIIAQYKPEEYSRF ||||||||||||||||| |||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ..GEEDIPREPRRIVIHRG.TGLGFNIIGGEDGEGIFISF.LAGGPADLSGELRKGDQILSVNGVDLRNASHEQAAIALKNAGQTVTIIAQYKPEEYSRF -- EA || EA
Dihedral angle restraints
-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400 FLGEEDIPREPRRIVIHRGSTGLGFNIIGGEDGEGIFISFXLAGGPADLSGELRKGDQILSVNGVDLRNASHEQAAIALKNAGQTVTIIAQYKPEEYSRF |||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| FLGEEDIPREPRRIVIHRGSTGLGFNIIGGEDGEGIFISF.LAGGPADLSGELRKGDQILSVNGVDLRNASHEQAAIALKNAGQTVTIIAQYKPEEYSRF -- EA || EA