cis form of a photoswitchable PDZ domain crosslinked with an azobenzene derivative
GPKPGDIFEV ELAKNDNSLG ICVTGGVNTS VRHGGIYVKA VIPQGAAESD GRIHKGDRVL AVNGVSLEGA THKQAVCTLR NTGQVVHLLL EKGQSPT
Polymer type: polypeptide(L)
Total | 1H | 13C | 15N | |
---|---|---|---|---|
All | 95.4 % (999 of 1047) | 95.4 % (514 of 539) | 97.0 % (394 of 406) | 89.2 % (91 of 102) |
Backbone | 97.6 % (560 of 574) | 99.0 % (202 of 204) | 96.4 % (267 of 277) | 97.8 % (91 of 93) |
Sidechain | 93.9 % (522 of 556) | 93.1 % (312 of 335) | 99.1 % (210 of 212) | 0.0 % (0 of 9) |
Aromatic | 91.2 % (31 of 34) | 94.1 % (16 of 17) | 88.2 % (15 of 17) | |
Methyl | 100.0 % (126 of 126) | 100.0 % (63 of 63) | 100.0 % (63 of 63) |
1. PDZ
GPKPGDIFEV ELAKNDNSLG ICVTGGVNTS VRHGGIYVKA VIPQGAAESD GRIHKGDRVL AVNGVSLEGA THKQAVCTLR NTGQVVHLLL EKGQSPTSolvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details sample used for measuring RDCs
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | PDZ | [U-100% 15N] | 0.75 mM | |
2 | sodium phosphate | natural abundance | 50 mM | |
3 | sodium chloride | natural abundance | 150 mM | |
4 | sodium azide | natural abundance | 0.1 mM | |
5 | C12E5 | natural abundance | 4.3 % | |
6 | n-hexanol | natural abundance | 1.8 % | |
7 | H2O | natural abundance | 90 % | |
8 | D2O | natural abundance | 10 % |
Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details sample used for measuring RDCs
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
9 | PDZ | [U-100% 15N] | 0.75 mM | |
10 | sodium phosphate | natural abundance | 50 mM | |
11 | sodium chloride | natural abundance | 150 mM | |
12 | sodium azide | natural abundance | 0.1 mM | |
13 | Pf1 phage | natural abundance | 8.5 mg/mL | |
14 | H2O | natural abundance | 90 % | |
15 | D2O | natural abundance | 10 % |
Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
16 | PDZ | [U-99% 13C; U-99% 15N] | 0.75 mM | |
17 | sodium phosphate | natural abundance | 50 mM | |
18 | sodium chloride | natural abundance | 150 mM | |
19 | sodium azide | natural abundance | 0.1 mM | |
20 | H2O | natural abundance | 90 % | |
21 | D2O | natural abundance | 10 % |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | water | protons | 4.71 ppm | internal | indirect | 0.2514495 |
1H | water | protons | 4.71 ppm | internal | direct | 1.0 |
15N | water | protons | 4.71 ppm | internal | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | water | protons | 4.71 ppm | internal | indirect | 0.2514495 |
1H | water | protons | 4.71 ppm | internal | direct | 1.0 |
15N | water | protons | 4.71 ppm | internal | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | water | protons | 4.71 ppm | internal | indirect | 0.2514495 |
1H | water | protons | 4.71 ppm | internal | direct | 1.0 |
15N | water | protons | 4.71 ppm | internal | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | water | protons | 4.71 ppm | internal | indirect | 0.2514495 |
1H | water | protons | 4.71 ppm | internal | direct | 1.0 |
15N | water | protons | 4.71 ppm | internal | indirect | 0.1013291 |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
16 | PDZ | [U-99% 13C; U-99% 15N] | 0.75 mM | |
17 | sodium phosphate | natural abundance | 50 mM | |
18 | sodium chloride | natural abundance | 150 mM | |
19 | sodium azide | natural abundance | 0.1 mM | |
20 | H2O | natural abundance | 90 % | |
21 | D2O | natural abundance | 10 % |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
16 | PDZ | [U-99% 13C; U-99% 15N] | 0.75 mM | |
17 | sodium phosphate | natural abundance | 50 mM | |
18 | sodium chloride | natural abundance | 150 mM | |
19 | sodium azide | natural abundance | 0.1 mM | |
20 | H2O | natural abundance | 90 % | |
21 | D2O | natural abundance | 10 % |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
16 | PDZ | [U-99% 13C; U-99% 15N] | 0.75 mM | |
17 | sodium phosphate | natural abundance | 50 mM | |
18 | sodium chloride | natural abundance | 150 mM | |
19 | sodium azide | natural abundance | 0.1 mM | |
20 | H2O | natural abundance | 90 % | |
21 | D2O | natural abundance | 10 % |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
16 | PDZ | [U-99% 13C; U-99% 15N] | 0.75 mM | |
17 | sodium phosphate | natural abundance | 50 mM | |
18 | sodium chloride | natural abundance | 150 mM | |
19 | sodium azide | natural abundance | 0.1 mM | |
20 | H2O | natural abundance | 90 % | |
21 | D2O | natural abundance | 10 % |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
16 | PDZ | [U-99% 13C; U-99% 15N] | 0.75 mM | |
17 | sodium phosphate | natural abundance | 50 mM | |
18 | sodium chloride | natural abundance | 150 mM | |
19 | sodium azide | natural abundance | 0.1 mM | |
20 | H2O | natural abundance | 90 % | |
21 | D2O | natural abundance | 10 % |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
16 | PDZ | [U-99% 13C; U-99% 15N] | 0.75 mM | |
17 | sodium phosphate | natural abundance | 50 mM | |
18 | sodium chloride | natural abundance | 150 mM | |
19 | sodium azide | natural abundance | 0.1 mM | |
20 | H2O | natural abundance | 90 % | |
21 | D2O | natural abundance | 10 % |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
16 | PDZ | [U-99% 13C; U-99% 15N] | 0.75 mM | |
17 | sodium phosphate | natural abundance | 50 mM | |
18 | sodium chloride | natural abundance | 150 mM | |
19 | sodium azide | natural abundance | 0.1 mM | |
20 | H2O | natural abundance | 90 % | |
21 | D2O | natural abundance | 10 % |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
16 | PDZ | [U-99% 13C; U-99% 15N] | 0.75 mM | |
17 | sodium phosphate | natural abundance | 50 mM | |
18 | sodium chloride | natural abundance | 150 mM | |
19 | sodium azide | natural abundance | 0.1 mM | |
20 | H2O | natural abundance | 90 % | |
21 | D2O | natural abundance | 10 % |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
16 | PDZ | [U-99% 13C; U-99% 15N] | 0.75 mM | |
17 | sodium phosphate | natural abundance | 50 mM | |
18 | sodium chloride | natural abundance | 150 mM | |
19 | sodium azide | natural abundance | 0.1 mM | |
20 | H2O | natural abundance | 90 % | |
21 | D2O | natural abundance | 10 % |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
16 | PDZ | [U-99% 13C; U-99% 15N] | 0.75 mM | |
17 | sodium phosphate | natural abundance | 50 mM | |
18 | sodium chloride | natural abundance | 150 mM | |
19 | sodium azide | natural abundance | 0.1 mM | |
20 | H2O | natural abundance | 90 % | |
21 | D2O | natural abundance | 10 % |
Bruker Avance - 600 MHz
State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details sample used for measuring RDCs
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
9 | PDZ | [U-100% 15N] | 0.75 mM | |
10 | sodium phosphate | natural abundance | 50 mM | |
11 | sodium chloride | natural abundance | 150 mM | |
12 | sodium azide | natural abundance | 0.1 mM | |
13 | Pf1 phage | natural abundance | 8.5 mg/mL | |
14 | H2O | natural abundance | 90 % | |
15 | D2O | natural abundance | 10 % |
Bruker Avance - 600 MHz
State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details sample used for measuring RDCs
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | PDZ | [U-100% 15N] | 0.75 mM | |
2 | sodium phosphate | natural abundance | 50 mM | |
3 | sodium chloride | natural abundance | 150 mM | |
4 | sodium azide | natural abundance | 0.1 mM | |
5 | C12E5 | natural abundance | 4.3 % | |
6 | n-hexanol | natural abundance | 1.8 % | |
7 | H2O | natural abundance | 90 % | |
8 | D2O | natural abundance | 10 % |
Properties
Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints | combined_18833_2m0z.nef |
Input source #2: Coordindates | 2m0z.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…) |
---|---|---|---|---|
1:22:CYS:SG | 2:1:33B:C1 | unknown | unknown | n/a |
1:77:CYS:SG | 2:1:33B:C20 | unknown | unknown | n/a |
Non-standard residues
Chain_ID | Seq_ID | Comp_ID | Chem_comp_name | Experimental evidences |
---|---|---|---|---|
B | 1 | 33B | 3,3'-(E)-diazene-1,2-diylbis{6-[(chloroacetyl)amino]benzenesulfonic acid} | None |
Sequence alignments
--------10--------20--------30--------40--------50--------60--------70--------80--------90------- GPKPGDIFEVELAKNDNSLGICVTGGVNTSVRHGGIYVKAVIPQGAAESDGRIHKGDRVLAVNGVSLEGATHKQAVCTLRNTGQVVHLLLEKGQSPT ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| GPKPGDIFEVELAKNDNSLGICVTGGVNTSVRHGGIYVKAVIPQGAAESDGRIHKGDRVLAVNGVSLEGATHKQAVCTLRNTGQVVHLLLEKGQSPT
Chain assignments
Entity_assembly_ID (NMR) | Auth_asym_ID (model) | Length | Unmapped | Conflict | Sequence coverage (%) |
---|---|---|---|---|---|
A | A | 97 | 0 | 0 | 100.0 |
Content subtype: combined_18833_2m0z.nef
Assigned chemical shifts
--------10--------20--------30--------40--------50--------60--------70--------80--------90------- GPKPGDIFEVELAKNDNSLGICVTGGVNTSVRHGGIYVKAVIPQGAAESDGRIHKGDRVLAVNGVSLEGATHKQAVCTLRNTGQVVHLLLEKGQSPT ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| GPKPGDIFEVELAKNDNSLGICVTGGVNTSVRHGGIYVKAVIPQGAAESDGRIHKGDRVLAVNGVSLEGATHKQAVCTLRNTGQVVHLLLEKGQSPT
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 539 | 513 | 95.2 |
13C chemical shifts | 406 | 394 | 97.0 |
15N chemical shifts | 106 | 90 | 84.9 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 204 | 201 | 98.5 |
13C chemical shifts | 194 | 184 | 94.8 |
15N chemical shifts | 93 | 90 | 96.8 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 335 | 312 | 93.1 |
13C chemical shifts | 212 | 210 | 99.1 |
15N chemical shifts | 13 | 0 | 0.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 63 | 63 | 100.0 |
13C chemical shifts | 63 | 63 | 100.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 17 | 16 | 94.1 |
13C chemical shifts | 17 | 15 | 88.2 |
Covalent bonds
Distance restraints
--------10--------20--------30--------40--------50--------60--------70--------80--------90------- GPKPGDIFEVELAKNDNSLGICVTGGVNTSVRHGGIYVKAVIPQGAAESDGRIHKGDRVLAVNGVSLEGATHKQAVCTLRNTGQVVHLLLEKGQSPT |||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| GPKPGDIFEVELAKNDNSLGICVTGGVNTSVR.GGIYVKAVIPQGAAESDGRIHKGDRVLAVNGVSLEGATHKQAVCTLRNTGQVVHLLLEKGQSPT
Dihedral angle restraints
--------10--------20--------30--------40--------50--------60--------70--------80--------90------- GPKPGDIFEVELAKNDNSLGICVTGGVNTSVRHGGIYVKAVIPQGAAESDGRIHKGDRVLAVNGVSLEGATHKQAVCTLRNTGQVVHLLLEKGQSPT |||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| .PKPGDIFEVELAKN.NSLGICVTGGVNTSVRHGGIYVKAVIPQGAAESDGRIHKGDRVLAVNGVSLEGATHKQAVCTLRNTGQVVHLLLEKGQSP --------10--------20--------30--------40--------50--------60--------70--------80--------90------
RDC restraints
--------10--------20--------30--------40--------50--------60--------70--------80--------90------- GPKPGDIFEVELAKNDNSLGICVTGGVNTSVRHGGIYVKAVIPQGAAESDGRIHKGDRVLAVNGVSLEGATHKQAVCTLRNTGQVVHLLLEKGQSPT | ||||||| ||| | |||||||||| || || ||||| ||| |||||| || |||||||| |||||| ||||| || ||||||||||| | ..K.GDIFEVE.AKN..S.GICVTGGVNT.VR.GG..VKAVI.QGA.ESDGRI.KG...LAVNGVSL.GATHKQ.VCTLR.TG.VVHLLLEKGQS.T