Solution NMR Structure of Ribosome Modulation Factor VP1593 from Vibrio parahaemolyticus. Northeast Structural Genomics Target VpR55
Polymer type: polypeptide(L)
Total | 1H | 13C | 15N | |
---|---|---|---|---|
All | 89.3 % (699 of 783) | 89.0 % (373 of 419) | 89.0 % (258 of 290) | 91.9 % (68 of 74) |
Backbone | 90.7 % (352 of 388) | 91.1 % (123 of 135) | 90.5 % (171 of 189) | 90.6 % (58 of 64) |
Sidechain | 88.1 % (400 of 454) | 88.0 % (250 of 284) | 87.5 % (140 of 160) | 100.0 % (10 of 10) |
Aromatic | 70.0 % (56 of 80) | 70.0 % (28 of 40) | 68.4 % (26 of 38) | 100.0 % (2 of 2) |
Methyl | 100.0 % (34 of 34) | 100.0 % (17 of 17) | 100.0 % (17 of 17) |
1. VpR55
MKRQKRDRLE RAQSQGYKAG LNGRSQEACP YQQVDARSYW LGGWRDARDE KQSGLYKLEH HHHHHSolvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 393 K, pH 6.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | VpR55 | [U-100% 13C; U-100% 15N] | 1.1 mM | |
2 | MES | natural abundance | 20 mM | |
3 | NaCl | natural abundance | 100 mM | |
4 | CaCl2 | natural abundance | 5 mM | |
5 | DTT | natural abundance | 10 mM | |
6 | NaN3 | natural abundance | 0.02 % |
Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 393 K, pH 6.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
7 | VpR55 | [U-5% 13C; U-100% 15N] | 1.1 mM | |
8 | MES | natural abundance | 20 mM | |
9 | NaCl | natural abundance | 100 mM | |
10 | CaCl2 | natural abundance | 5 mM | |
11 | DTT | natural abundance | 10 mM | |
12 | NaN3 | natural abundance | 0.02 % |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | external | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | external | indirect | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | external | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | external | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | external | indirect | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | external | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | external | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | external | indirect | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | external | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | external | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | external | indirect | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | external | indirect | 0.1013291 |
Bruker Avance - 800 MHz cryoprobe
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 393 K, pH 6.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | VpR55 | [U-100% 13C; U-100% 15N] | 1.1 mM | |
2 | MES | natural abundance | 20 mM | |
3 | NaCl | natural abundance | 100 mM | |
4 | CaCl2 | natural abundance | 5 mM | |
5 | DTT | natural abundance | 10 mM | |
6 | NaN3 | natural abundance | 0.02 % |
Bruker Avance - 800 MHz cryoprobe
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 393 K, pH 6.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | VpR55 | [U-100% 13C; U-100% 15N] | 1.1 mM | |
2 | MES | natural abundance | 20 mM | |
3 | NaCl | natural abundance | 100 mM | |
4 | CaCl2 | natural abundance | 5 mM | |
5 | DTT | natural abundance | 10 mM | |
6 | NaN3 | natural abundance | 0.02 % |
Bruker Avance - 800 MHz cryoprobe
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 393 K, pH 6.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | VpR55 | [U-100% 13C; U-100% 15N] | 1.1 mM | |
2 | MES | natural abundance | 20 mM | |
3 | NaCl | natural abundance | 100 mM | |
4 | CaCl2 | natural abundance | 5 mM | |
5 | DTT | natural abundance | 10 mM | |
6 | NaN3 | natural abundance | 0.02 % |
Bruker Avance - 800 MHz cryoprobe
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 393 K, pH 6.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | VpR55 | [U-100% 13C; U-100% 15N] | 1.1 mM | |
2 | MES | natural abundance | 20 mM | |
3 | NaCl | natural abundance | 100 mM | |
4 | CaCl2 | natural abundance | 5 mM | |
5 | DTT | natural abundance | 10 mM | |
6 | NaN3 | natural abundance | 0.02 % |
Bruker Avance - 800 MHz cryoprobe
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 393 K, pH 6.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | VpR55 | [U-100% 13C; U-100% 15N] | 1.1 mM | |
2 | MES | natural abundance | 20 mM | |
3 | NaCl | natural abundance | 100 mM | |
4 | CaCl2 | natural abundance | 5 mM | |
5 | DTT | natural abundance | 10 mM | |
6 | NaN3 | natural abundance | 0.02 % |
Bruker Avance - 800 MHz cryoprobe
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 393 K, pH 6.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | VpR55 | [U-100% 13C; U-100% 15N] | 1.1 mM | |
2 | MES | natural abundance | 20 mM | |
3 | NaCl | natural abundance | 100 mM | |
4 | CaCl2 | natural abundance | 5 mM | |
5 | DTT | natural abundance | 10 mM | |
6 | NaN3 | natural abundance | 0.02 % |
Bruker Avance - 800 MHz cryoprobe
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 393 K, pH 6.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | VpR55 | [U-100% 13C; U-100% 15N] | 1.1 mM | |
2 | MES | natural abundance | 20 mM | |
3 | NaCl | natural abundance | 100 mM | |
4 | CaCl2 | natural abundance | 5 mM | |
5 | DTT | natural abundance | 10 mM | |
6 | NaN3 | natural abundance | 0.02 % |
Bruker Avance - 800 MHz cryoprobe
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 393 K, pH 6.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | VpR55 | [U-100% 13C; U-100% 15N] | 1.1 mM | |
2 | MES | natural abundance | 20 mM | |
3 | NaCl | natural abundance | 100 mM | |
4 | CaCl2 | natural abundance | 5 mM | |
5 | DTT | natural abundance | 10 mM | |
6 | NaN3 | natural abundance | 0.02 % |
Bruker Avance - 800 MHz cryoprobe
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 393 K, pH 6.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | VpR55 | [U-100% 13C; U-100% 15N] | 1.1 mM | |
2 | MES | natural abundance | 20 mM | |
3 | NaCl | natural abundance | 100 mM | |
4 | CaCl2 | natural abundance | 5 mM | |
5 | DTT | natural abundance | 10 mM | |
6 | NaN3 | natural abundance | 0.02 % |
Bruker Avance - 800 MHz cryoprobe
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 393 K, pH 6.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | VpR55 | [U-100% 13C; U-100% 15N] | 1.1 mM | |
2 | MES | natural abundance | 20 mM | |
3 | NaCl | natural abundance | 100 mM | |
4 | CaCl2 | natural abundance | 5 mM | |
5 | DTT | natural abundance | 10 mM | |
6 | NaN3 | natural abundance | 0.02 % |
Bruker Avance - 800 MHz cryoprobe
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 393 K, pH 6.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | VpR55 | [U-100% 13C; U-100% 15N] | 1.1 mM | |
2 | MES | natural abundance | 20 mM | |
3 | NaCl | natural abundance | 100 mM | |
4 | CaCl2 | natural abundance | 5 mM | |
5 | DTT | natural abundance | 10 mM | |
6 | NaN3 | natural abundance | 0.02 % |
Bruker Avance - 800 MHz cryoprobe
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 393 K, pH 6.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | VpR55 | [U-100% 13C; U-100% 15N] | 1.1 mM | |
2 | MES | natural abundance | 20 mM | |
3 | NaCl | natural abundance | 100 mM | |
4 | CaCl2 | natural abundance | 5 mM | |
5 | DTT | natural abundance | 10 mM | |
6 | NaN3 | natural abundance | 0.02 % |
Bruker Avance - 800 MHz cryoprobe
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 393 K, pH 6.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
7 | VpR55 | [U-5% 13C; U-100% 15N] | 1.1 mM | |
8 | MES | natural abundance | 20 mM | |
9 | NaCl | natural abundance | 100 mM | |
10 | CaCl2 | natural abundance | 5 mM | |
11 | DTT | natural abundance | 10 mM | |
12 | NaN3 | natural abundance | 0.02 % |
Properties
Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints | combined_15339_2jrm.nef |
Input source #2: Coordindates | 2jrm.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 | None |
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)
NoneNon-standard residues
NoneSequence alignments
--------10--------20--------30--------40--------50--------60----- MKRQKRDRLERAQSQGYKAGLNGRSQEACPYQQVDARSYWLGGWRDARDEKQSGLYKLEHHHHHH ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| MKRQKRDRLERAQSQGYKAGLNGRSQEACPYQQVDARSYWLGGWRDARDEKQSGLYKLEHHHHHH
Chain assignments
Entity_assembly_ID (NMR) | Auth_asym_ID (model) | Length | Unmapped | Conflict | Sequence coverage (%) |
---|---|---|---|---|---|
A | A | 65 | 0 | 0 | 100.0 |
Content subtype: combined_15339_2jrm.nef
Assigned chemical shifts
--------10--------20--------30--------40--------50--------60----- MKRQKRDRLERAQSQGYKAGLNGRSQEACPYQQVDARSYWLGGWRDARDEKQSGLYKLEHHHHHH |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| MKRQKRDRLERAQSQGYKAGLNGRSQEACPYQQVDARSYWLGGWRDARDEKQSGLYKLEH --------10--------20--------30--------40--------50--------60
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 419 | 373 | 89.0 |
13C chemical shifts | 290 | 258 | 89.0 |
15N chemical shifts | 82 | 71 | 86.6 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 135 | 123 | 91.1 |
13C chemical shifts | 130 | 118 | 90.8 |
15N chemical shifts | 64 | 58 | 90.6 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 284 | 250 | 88.0 |
13C chemical shifts | 160 | 140 | 87.5 |
15N chemical shifts | 18 | 13 | 72.2 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 18 | 17 | 94.4 |
13C chemical shifts | 18 | 17 | 94.4 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 40 | 28 | 70.0 |
13C chemical shifts | 38 | 26 | 68.4 |
15N chemical shifts | 2 | 2 | 100.0 |
Distance restraints
--------10--------20--------30--------40--------50--------60----- MKRQKRDRLERAQSQGYKAGLNGRSQEACPYQQVDARSYWLGGWRDARDEKQSGLYKLEHHHHHH |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| MKRQKRDRLERAQSQGYKAGLNGRSQEACPYQQVDARSYWLGGWRDARDEKQSGLYKLEH --------10--------20--------30--------40--------50--------60
--------10--------20--------30--------40--------50--------60----- MKRQKRDRLERAQSQGYKAGLNGRSQEACPYQQVDARSYWLGGWRDARDEKQSGLYKLEHHHHHH |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| MKRQKRDRLERAQSQGYKAGLNGRSQEACPYQQVDARSYWLGGWRDARDEKQSGLYKLEH --------10--------20--------30--------40--------50--------60
--------10--------20--------30--------40--------50--------60----- MKRQKRDRLERAQSQGYKAGLNGRSQEACPYQQVDARSYWLGGWRDARDEKQSGLYKLEHHHHHH ||| |||||| ||| || ||||||||||||||||||||| ......DRL.RAQSQG.KAG.NG.........QVDARSYWLGGWRDARDEKQS --------10--------20--------30--------40--------50---
--------10--------20--------30--------40--------50--------60----- MKRQKRDRLERAQSQGYKAGLNGRSQEACPYQQVDARSYWLGGWRDARDEKQSGLYKLEHHHHHH ||| |||||| ||| || ||||||||||||||||||||| ......DRL.RAQSQG.KAG.NG.........QVDARSYWLGGWRDARDEKQS --------10--------20--------30--------40--------50---
Dihedral angle restraints
--------10--------20--------30--------40--------50--------60----- MKRQKRDRLERAQSQGYKAGLNGRSQEACPYQQVDARSYWLGGWRDARDEKQSGLYKLEHHHHHH ||||||||||||||||||||||||| |||||||||||||||||||||||| ...QKRDRLERAQSQGYKAGLNGRSQEA...QQVDARSYWLGGWRDARDEKQSGL --------10--------20--------30--------40--------50-----
--------10--------20--------30--------40--------50--------60----- MKRQKRDRLERAQSQGYKAGLNGRSQEACPYQQVDARSYWLGGWRDARDEKQSGLYKLEHHHHHH ||||||||||||||||||||||||| |||||||||||||||||||||||| ...QKRDRLERAQSQGYKAGLNGRSQEA...QQVDARSYWLGGWRDARDEKQSGL --------10--------20--------30--------40--------50-----