Solution NMR structure of the R2R3 DNA binding domain of Myb1 protein from protozoan parasite Trichomonas vaginalis
KVKFTEEEDL KLQQLVMRYG AKDWIRISQL MITRNPRQCR ERWNNYINPA LRTDPWSPEE DMLLDQKYAE YGPKWNKISK FLKNRSDNNI RNRWMMIARH RAKHQKS
Polymer type: polypeptide(L)
Total | 1H | 13C | 15N | |
---|---|---|---|---|
All | 95.6 % (1318 of 1378) | 95.1 % (704 of 740) | 95.9 % (495 of 516) | 97.5 % (119 of 122) |
Backbone | 97.9 % (619 of 632) | 97.6 % (206 of 211) | 98.4 % (314 of 319) | 97.1 % (99 of 102) |
Sidechain | 94.2 % (802 of 851) | 94.1 % (498 of 529) | 94.0 % (284 of 302) | 100.0 % (20 of 20) |
Aromatic | 81.7 % (98 of 120) | 81.7 % (49 of 60) | 80.0 % (44 of 55) | 100.0 % (5 of 5) |
Methyl | 97.6 % (82 of 84) | 97.6 % (41 of 42) | 97.6 % (41 of 42) |
1. R2R3 DNA binding domain
KVKFTEEEDL KLQQLVMRYG AKDWIRISQL MITRNPRQCR ERWNNYINPA LRTDPWSPEE DMLLDQKYAE YGPKWNKISK FLKNRSDNNI RNRWMMIARH RAKHQKSSolvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity | [U-13C; U-15N] | 1 mM | |
2 | sodium chloride | natural abundance | 50 mM | |
3 | sodium phosphate | natural abundance | 20 mM | |
4 | sodium azide | natural abundance | 5 mM | |
5 | beta-mercaptoethanol | natural abundance | 20 mM |
Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
6 | entity | [U-13C; U-15N] | 1 mM | |
7 | sodium chloride | natural abundance | 50 mM | |
8 | sodium phosphate | natural abundance | 20 mM | |
9 | sodium azide | natural abundance | 5 mM | |
10 | beta-mercaptoethanol | natural abundance | 20 mM |
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 |
Pressure 1 atm, Temperature 298 K, pH 6.0
Experiment name 2D 1H-15N HxNOE
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity | [U-13C; U-15N] | 1 mM | |
2 | sodium chloride | natural abundance | 50 mM | |
3 | sodium phosphate | natural abundance | 20 mM | |
4 | sodium azide | natural abundance | 5 mM | |
5 | beta-mercaptoethanol | natural abundance | 20 mM |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity | [U-13C; U-15N] | 1 mM | |
2 | sodium chloride | natural abundance | 50 mM | |
3 | sodium phosphate | natural abundance | 20 mM | |
4 | sodium azide | natural abundance | 5 mM | |
5 | beta-mercaptoethanol | natural abundance | 20 mM |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity | [U-13C; U-15N] | 1 mM | |
2 | sodium chloride | natural abundance | 50 mM | |
3 | sodium phosphate | natural abundance | 20 mM | |
4 | sodium azide | natural abundance | 5 mM | |
5 | beta-mercaptoethanol | natural abundance | 20 mM |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity | [U-13C; U-15N] | 1 mM | |
2 | sodium chloride | natural abundance | 50 mM | |
3 | sodium phosphate | natural abundance | 20 mM | |
4 | sodium azide | natural abundance | 5 mM | |
5 | beta-mercaptoethanol | natural abundance | 20 mM |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity | [U-13C; U-15N] | 1 mM | |
2 | sodium chloride | natural abundance | 50 mM | |
3 | sodium phosphate | natural abundance | 20 mM | |
4 | sodium azide | natural abundance | 5 mM | |
5 | beta-mercaptoethanol | natural abundance | 20 mM |
Bruker Avance - 800 MHz
State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
6 | entity | [U-13C; U-15N] | 1 mM | |
7 | sodium chloride | natural abundance | 50 mM | |
8 | sodium phosphate | natural abundance | 20 mM | |
9 | sodium azide | natural abundance | 5 mM | |
10 | beta-mercaptoethanol | natural abundance | 20 mM |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity | [U-13C; U-15N] | 1 mM | |
2 | sodium chloride | natural abundance | 50 mM | |
3 | sodium phosphate | natural abundance | 20 mM | |
4 | sodium azide | natural abundance | 5 mM | |
5 | beta-mercaptoethanol | natural abundance | 20 mM |
Bruker Avance - 800 MHz
State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
6 | entity | [U-13C; U-15N] | 1 mM | |
7 | sodium chloride | natural abundance | 50 mM | |
8 | sodium phosphate | natural abundance | 20 mM | |
9 | sodium azide | natural abundance | 5 mM | |
10 | beta-mercaptoethanol | natural abundance | 20 mM |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity | [U-13C; U-15N] | 1 mM | |
2 | sodium chloride | natural abundance | 50 mM | |
3 | sodium phosphate | natural abundance | 20 mM | |
4 | sodium azide | natural abundance | 5 mM | |
5 | beta-mercaptoethanol | natural abundance | 20 mM |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity | [U-13C; U-15N] | 1 mM | |
2 | sodium chloride | natural abundance | 50 mM | |
3 | sodium phosphate | natural abundance | 20 mM | |
4 | sodium azide | natural abundance | 5 mM | |
5 | beta-mercaptoethanol | natural abundance | 20 mM |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity | [U-13C; U-15N] | 1 mM | |
2 | sodium chloride | natural abundance | 50 mM | |
3 | sodium phosphate | natural abundance | 20 mM | |
4 | sodium azide | natural abundance | 5 mM | |
5 | beta-mercaptoethanol | natural abundance | 20 mM |
Properties
Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints | combined_15989_2k9n.nef |
Input source #2: Coordindates | 2k9n.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--------70--------80--------90-------100 KVKFTEEEDLKLQQLVMRYGAKDWIRISQLMITRNPRQCRERWNNYINPALRTDPWSPEEDMLLDQKYAEYGPKWNKISKFLKNRSDNNIRNRWMMIARH |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| KVKFTEEEDLKLQQLVMRYGAKDWIRISQLMITRNPRQCRERWNNYINPALRTDPWSPEEDMLLDQKYAEYGPKWNKISKFLKNRSDNNIRNRWMMIARH ------- RAKHQKS ||||||| RAKHQKS
Chain assignments
Entity_assembly_ID (NMR) | Auth_asym_ID (model) | Length | Unmapped | Conflict | Sequence coverage (%) |
---|---|---|---|---|---|
A | A | 107 | 0 | 0 | 100.0 |
Content subtype: combined_15989_2k9n.nef
Assigned chemical shifts
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 KVKFTEEEDLKLQQLVMRYGAKDWIRISQLMITRNPRQCRERWNNYINPALRTDPWSPEEDMLLDQKYAEYGPKWNKISKFLKNRSDNNIRNRWMMIARH |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| KVKFTEEEDLKLQQLVMRYGAKDWIRISQLMITRNPRQCRERWNNYINPALRTDPWSPEEDMLLDQKYAEYGPKWNKISKFLKNRSDNNIRNRWMMIARH ------- RAKHQKS ||||||| RAKHQKS
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 740 | 705 | 95.3 |
13C chemical shifts | 516 | 493 | 95.5 |
15N chemical shifts | 134 | 121 | 90.3 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 211 | 208 | 98.6 |
13C chemical shifts | 214 | 211 | 98.6 |
15N chemical shifts | 102 | 99 | 97.1 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 529 | 497 | 94.0 |
13C chemical shifts | 302 | 282 | 93.4 |
15N chemical shifts | 32 | 22 | 68.8 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 47 | 42 | 89.4 |
13C chemical shifts | 47 | 41 | 87.2 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 60 | 49 | 81.7 |
13C chemical shifts | 55 | 44 | 80.0 |
15N chemical shifts | 5 | 5 | 100.0 |
Distance restraints
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 KVKFTEEEDLKLQQLVMRYGAKDWIRISQLMITRNPRQCRERWNNYINPALRTDPWSPEEDMLLDQKYAEYGPKWNKISKFLKNRSDNNIRNRWMMIARH |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| KVKFTEEEDLKLQQLVMRYGAKDWIRISQLMITRNPRQCRERWNNYINPALRTDPWSPEEDMLLDQKYAEYGPKWNKISKFLKNRSDNNIRNRWMMIARH ------- RAKHQKS ||||||| RAKHQKS
Dihedral angle restraints
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 KVKFTEEEDLKLQQLVMRYGAKDWIRISQLMITRNPRQCRERWNNYINPALRTDPWSPEEDMLLDQKYAEYGPKWNKISKFLKNRSDNNIRNRWMMIARH ||||||||||||||||| |||||||||| |||||||||||||||| ||||||||||||||||| |||||||| ||||||||||||||||| ...FTEEEDLKLQQLVMRYG.KDWIRISQLM.TRNPRQCRERWNNYIN.......WSPEEDMLLDQKYAEYG.KWNKISKF..NRSDNNIRNRWMMIARH --------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 ------- RAKHQKS || RA --