Solution structure of RPA3114, a SEC-C motif containing protein from Rhodopseudomonas palustris; Northeast Structural Genomics Consortium target RpT5 / Ontario Center for Structural Proteomics target RP3097
MNCVCGSGKT YDDCCGPLLA RTRSAASPEA LMRSRYAAYA LKDFDYIVET TDPERRDLFD HDVNRAWMEE SDFLELRVLG SSEKGSRGTV EFIARFRRGG GPEQSHHERS QFRKARGRWY FSEGEAVD
Polymer type: polypeptide(L)
Total | 1H | 13C | 15N | |
---|---|---|---|---|
All | 92.2 % (1340 of 1453) | 92.0 % (699 of 760) | 91.8 % (517 of 563) | 95.4 % (124 of 130) |
Backbone | 95.8 % (728 of 760) | 95.8 % (252 of 263) | 95.7 % (357 of 373) | 96.0 % (119 of 124) |
Sidechain | 89.8 % (727 of 810) | 89.9 % (447 of 497) | 89.6 % (275 of 307) | 83.3 % (5 of 6) |
Aromatic | 71.9 % (105 of 146) | 76.7 % (56 of 73) | 67.6 % (48 of 71) | 50.0 % (1 of 2) |
Methyl | 99.0 % (95 of 96) | 97.9 % (47 of 48) | 100.0 % (48 of 48) |
1. RP3097
MNCVCGSGKT YDDCCGPLLA RTRSAASPEA LMRSRYAAYA LKDFDYIVET TDPERRDLFD HDVNRAWMEE SDFLELRVLG SSEKGSRGTV EFIARFRRGG GPEQSHHERS QFRKARGRWY FSEGEAVDSolvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity_1 | [U-13C; U-15N] | 0.5 mM | |
2 | TRIS | [U-99% 2H] | 10 mM | |
3 | DTT | [U-99% 2H] | 10 mM | |
4 | sodium chloride | natural abundance | 300 mM | |
5 | sodium azide | natural abundance | 0.1 % | |
6 | benzamidine | natural abundance | 1 mM | |
7 | ZnS04 | natural abundance | 10 uM | |
8 | H2O | 95 % | ||
9 | D2O | 5 % |
Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
10 | entity_1 | [U-13C; U-15N] | 0.5 mM | |
11 | TRIS | [U-99% 2H] | 10 mM | |
12 | DTT | [U-99% 2H] | 10 mM | |
13 | sodium chloride | natural abundance | 300 mM | |
14 | sodium azide | natural abundance | 0.1 % | |
15 | benzamidine | natural abundance | 1 mM | |
16 | ZnS04 | natural abundance | 10 uM | |
17 | D2O | 100 % |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | null | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | null | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | null | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | null | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | null | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | null | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | null | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | null | indirect | 0.1013291 |
Varian INOVA - 500 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity_1 | [U-13C; U-15N] | 0.5 mM | |
2 | TRIS | [U-99% 2H] | 10 mM | |
3 | DTT | [U-99% 2H] | 10 mM | |
4 | sodium chloride | natural abundance | 300 mM | |
5 | sodium azide | natural abundance | 0.1 % | |
6 | benzamidine | natural abundance | 1 mM | |
7 | ZnS04 | natural abundance | 10 uM | |
8 | H2O | 95 % | ||
9 | D2O | 5 % |
Varian INOVA - 500 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity_1 | [U-13C; U-15N] | 0.5 mM | |
2 | TRIS | [U-99% 2H] | 10 mM | |
3 | DTT | [U-99% 2H] | 10 mM | |
4 | sodium chloride | natural abundance | 300 mM | |
5 | sodium azide | natural abundance | 0.1 % | |
6 | benzamidine | natural abundance | 1 mM | |
7 | ZnS04 | natural abundance | 10 uM | |
8 | H2O | 95 % | ||
9 | D2O | 5 % |
Varian INOVA - 500 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity_1 | [U-13C; U-15N] | 0.5 mM | |
2 | TRIS | [U-99% 2H] | 10 mM | |
3 | DTT | [U-99% 2H] | 10 mM | |
4 | sodium chloride | natural abundance | 300 mM | |
5 | sodium azide | natural abundance | 0.1 % | |
6 | benzamidine | natural abundance | 1 mM | |
7 | ZnS04 | natural abundance | 10 uM | |
8 | H2O | 95 % | ||
9 | D2O | 5 % |
Varian INOVA - 500 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity_1 | [U-13C; U-15N] | 0.5 mM | |
2 | TRIS | [U-99% 2H] | 10 mM | |
3 | DTT | [U-99% 2H] | 10 mM | |
4 | sodium chloride | natural abundance | 300 mM | |
5 | sodium azide | natural abundance | 0.1 % | |
6 | benzamidine | natural abundance | 1 mM | |
7 | ZnS04 | natural abundance | 10 uM | |
8 | H2O | 95 % | ||
9 | D2O | 5 % |
Varian INOVA - 500 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity_1 | [U-13C; U-15N] | 0.5 mM | |
2 | TRIS | [U-99% 2H] | 10 mM | |
3 | DTT | [U-99% 2H] | 10 mM | |
4 | sodium chloride | natural abundance | 300 mM | |
5 | sodium azide | natural abundance | 0.1 % | |
6 | benzamidine | natural abundance | 1 mM | |
7 | ZnS04 | natural abundance | 10 uM | |
8 | H2O | 95 % | ||
9 | D2O | 5 % |
Varian INOVA - 500 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity_1 | [U-13C; U-15N] | 0.5 mM | |
2 | TRIS | [U-99% 2H] | 10 mM | |
3 | DTT | [U-99% 2H] | 10 mM | |
4 | sodium chloride | natural abundance | 300 mM | |
5 | sodium azide | natural abundance | 0.1 % | |
6 | benzamidine | natural abundance | 1 mM | |
7 | ZnS04 | natural abundance | 10 uM | |
8 | H2O | 95 % | ||
9 | D2O | 5 % |
Varian INOVA - 500 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity_1 | [U-13C; U-15N] | 0.5 mM | |
2 | TRIS | [U-99% 2H] | 10 mM | |
3 | DTT | [U-99% 2H] | 10 mM | |
4 | sodium chloride | natural abundance | 300 mM | |
5 | sodium azide | natural abundance | 0.1 % | |
6 | benzamidine | natural abundance | 1 mM | |
7 | ZnS04 | natural abundance | 10 uM | |
8 | H2O | 95 % | ||
9 | D2O | 5 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
10 | entity_1 | [U-13C; U-15N] | 0.5 mM | |
11 | TRIS | [U-99% 2H] | 10 mM | |
12 | DTT | [U-99% 2H] | 10 mM | |
13 | sodium chloride | natural abundance | 300 mM | |
14 | sodium azide | natural abundance | 0.1 % | |
15 | benzamidine | natural abundance | 1 mM | |
16 | ZnS04 | natural abundance | 10 uM | |
17 | D2O | 100 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
10 | entity_1 | [U-13C; U-15N] | 0.5 mM | |
11 | TRIS | [U-99% 2H] | 10 mM | |
12 | DTT | [U-99% 2H] | 10 mM | |
13 | sodium chloride | natural abundance | 300 mM | |
14 | sodium azide | natural abundance | 0.1 % | |
15 | benzamidine | natural abundance | 1 mM | |
16 | ZnS04 | natural abundance | 10 uM | |
17 | D2O | 100 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
10 | entity_1 | [U-13C; U-15N] | 0.5 mM | |
11 | TRIS | [U-99% 2H] | 10 mM | |
12 | DTT | [U-99% 2H] | 10 mM | |
13 | sodium chloride | natural abundance | 300 mM | |
14 | sodium azide | natural abundance | 0.1 % | |
15 | benzamidine | natural abundance | 1 mM | |
16 | ZnS04 | natural abundance | 10 uM | |
17 | D2O | 100 % |
Properties
Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints | combined_15270_2jq5.nef |
Input source #2: Coordindates | 2jq5.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…) |
---|---|---|---|---|
2:1:ZN:ZN | 1:3:CYS:SG | unknown | unknown | n/a |
2:1:ZN:ZN | 1:5:CYS:SG | unknown | unknown | n/a |
2:1:ZN:ZN | 1:14:CYS:SG | unknown | unknown | n/a |
2:1:ZN:ZN | 1:15:CYS:SG | 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--------60--------70--------80--------90-------100 MNCVCGSGKTYDDCCGPLLARTRSAASPEALMRSRYAAYALKDFDYIVETTDPERRDLFDHDVNRAWMEESDFLELRVLGSSEKGSRGTVEFIARFRRGG |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| MNCVCGSGKTYDDCCGPLLARTRSAASPEALMRSRYAAYALKDFDYIVETTDPERRDLFDHDVNRAWMEESDFLELRVLGSSEKGSRGTVEFIARFRRGG -------110-------120-------- GPEQSHHERSQFRKARGRWYFSEGEAVD |||||||||||||||||||||||||||| GPEQSHHERSQFRKARGRWYFSEGEAVD
Chain assignments
Entity_assembly_ID (NMR) | Auth_asym_ID (model) | Length | Unmapped | Conflict | Sequence coverage (%) |
---|---|---|---|---|---|
A | A | 128 | 0 | 0 | 100.0 |
Content subtype: combined_15270_2jq5.nef
Assigned chemical shifts
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 MNCVCGSGKTYDDCCGPLLARTRSAASPEALMRSRYAAYALKDFDYIVETTDPERRDLFDHDVNRAWMEESDFLELRVLGSSEKGSRGTVEFIARFRRGG ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||| MNCVCGSGKTYDDCCGPLLARTRSAASPEALMRSRYAAYALKDFDYIVETTDPERRDLF.HDVNRAWMEESDFLELRVLGSSEKGSRGTVEFIARFRRGG -------110-------120-------- GPEQSHHERSQFRKARGRWYFSEGEAVD |||||||||||||||||||||||||||| GPEQSHHERSQFRKARGRWYFSEGEAVD
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 760 | 702 | 92.4 |
13C chemical shifts | 563 | 515 | 91.5 |
15N chemical shifts | 146 | 121 | 82.9 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 263 | 252 | 95.8 |
13C chemical shifts | 256 | 241 | 94.1 |
15N chemical shifts | 124 | 116 | 93.5 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 497 | 450 | 90.5 |
13C chemical shifts | 307 | 274 | 89.3 |
15N chemical shifts | 22 | 5 | 22.7 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 51 | 48 | 94.1 |
13C chemical shifts | 51 | 48 | 94.1 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 73 | 56 | 76.7 |
13C chemical shifts | 71 | 48 | 67.6 |
15N chemical shifts | 2 | 1 | 50.0 |
Covalent bonds
Distance restraints
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 MNCVCGSGKTYDDCCGPLLARTRSAASPEALMRSRYAAYALKDFDYIVETTDPERRDLFDHDVNRAWMEESDFLELRVLGSSEKGSRGTVEFIARFRRGG ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||| MNCVCGSGKTYDDCCGPLLARTRSAASPEALMRSRYAAYALKDFDYIVETTDPERRDLF.HDVNRAWMEESDFLELRVLGSSEKGSRGTVEFIARFRRGG -------110-------120-------- GPEQSHHERSQFRKARGRWYFSEGEAVD |||||||||||||||||||||||||||| GPEQSHHERSQFRKARGRWYFSEGEAVD
Dihedral angle restraints
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 MNCVCGSGKTYDDCCGPLLARTRSAASPEALMRSRYAAYALKDFDYIVETTDPERRDLFDHDVNRAWMEESDFLELRVLGSSEKGSRGTVEFIARFRRGG |||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| .......GKTYDDCCGPLLARTRSA..PEALMRSRYAAYALKDFDYIVETTDPERRDLFDHDVNRAWMEESDFLELRVLGSSEKGSRGTVEFIARFRRG. --------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 -------110-------120-------- GPEQSHHERSQFRKARGRWYFSEGEAVD ||||||||||||||||||||||||| ..EQSHHERSQFRKARGRWYFSEGEAV -------110-------120-------