Solution structure of Diiron protein in presence of 8 eq Zn2+, Northeast Structural Genomics consortium target OR21
MDELRELLKA EQQGIKILKE VLKKAKEGDE QELARLNQEI VKAEKQGVKV YKEAAEKARN PEKRQVIDKI LEDEEKHIEW HKAASKQGNA EQFASLVQQH LQDEQRHVEE IEKKN
Polymer type: polypeptide(L)
Total | 1H | 13C | 15N | |
---|---|---|---|---|
All | 90.8 % (1292 of 1423) | 97.6 % (745 of 763) | 79.6 % (421 of 529) | 96.2 % (126 of 131) |
Backbone | 83.3 % (573 of 688) | 97.0 % (226 of 233) | 69.8 % (238 of 341) | 95.6 % (109 of 114) |
Sidechain | 97.9 % (828 of 846) | 97.9 % (519 of 530) | 97.7 % (292 of 299) | 100.0 % (17 of 17) |
Aromatic | 91.3 % (42 of 46) | 100.0 % (23 of 23) | 81.8 % (18 of 22) | 100.0 % (1 of 1) |
Methyl | 100.0 % (118 of 118) | 100.0 % (59 of 59) | 100.0 % (59 of 59) |
1. Diiron
MDELRELLKA EQQGIKILKE VLKKAKEGDE QELARLNQEI VKAEKQGVKV YKEAAEKARN PEKRQVIDKI LEDEEKHIEW HKAASKQGNA EQFASLVQQH LQDEQRHVEE IEKKNSolvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.8
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Diiron | [U-100% 13C; U-100% 15N] | 0.8 mM | |
2 | H2O | natural abundance | 95.0 % | |
3 | D2O | natural abundance | 5.0 % |
Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.8
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
4 | Diiron | [U-10% 13C; U-100% 15N] | 0.3 mM | |
5 | H2O | natural abundance | 95.0 % | |
6 | D2O | natural abundance | 5.0 % |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | na | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | na | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | na | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | na | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | na | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | na | indirect | 0.1013291 |
Varian INOVA - 750 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.8
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Diiron | [U-100% 13C; U-100% 15N] | 0.8 mM | |
2 | H2O | natural abundance | 95.0 % | |
3 | D2O | natural abundance | 5.0 % |
Varian INOVA - 750 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.8
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Diiron | [U-100% 13C; U-100% 15N] | 0.8 mM | |
2 | H2O | natural abundance | 95.0 % | |
3 | D2O | natural abundance | 5.0 % |
Varian INOVA - 750 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.8
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
4 | Diiron | [U-10% 13C; U-100% 15N] | 0.3 mM | |
5 | H2O | natural abundance | 95.0 % | |
6 | D2O | natural abundance | 5.0 % |
Varian INOVA - 750 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.8
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Diiron | [U-100% 13C; U-100% 15N] | 0.8 mM | |
2 | H2O | natural abundance | 95.0 % | |
3 | D2O | natural abundance | 5.0 % |
Varian INOVA - 750 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.8
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Diiron | [U-100% 13C; U-100% 15N] | 0.8 mM | |
2 | H2O | natural abundance | 95.0 % | |
3 | D2O | natural abundance | 5.0 % |
Varian INOVA - 750 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.8
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Diiron | [U-100% 13C; U-100% 15N] | 0.8 mM | |
2 | H2O | natural abundance | 95.0 % | |
3 | D2O | natural abundance | 5.0 % |
Varian INOVA - 750 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.8
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Diiron | [U-100% 13C; U-100% 15N] | 0.8 mM | |
2 | H2O | natural abundance | 95.0 % | |
3 | D2O | natural abundance | 5.0 % |
Varian INOVA - 750 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.8
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Diiron | [U-100% 13C; U-100% 15N] | 0.8 mM | |
2 | H2O | natural abundance | 95.0 % | |
3 | D2O | natural abundance | 5.0 % |
Varian INOVA - 750 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.8
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Diiron | [U-100% 13C; U-100% 15N] | 0.8 mM | |
2 | H2O | natural abundance | 95.0 % | |
3 | D2O | natural abundance | 5.0 % |
Varian INOVA - 750 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.8
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Diiron | [U-100% 13C; U-100% 15N] | 0.8 mM | |
2 | H2O | natural abundance | 95.0 % | |
3 | D2O | natural abundance | 5.0 % |
Varian INOVA - 750 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.8
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Diiron | [U-100% 13C; U-100% 15N] | 0.8 mM | |
2 | H2O | natural abundance | 95.0 % | |
3 | D2O | natural abundance | 5.0 % |
Properties
Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints | combined_17751_2lff.nef |
Input source #2: Coordindates | 2lff.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 | Error |
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…) |
---|---|---|---|---|
1:77:HIS:ND1 | 2:2:ZN:ZN | unknown | unknown | n/a |
1:44:GLU:OE2 | 2:2:ZN:ZN | unknown | unknown | n/a |
1:107:HIS:ND1 | 2:3:ZN:ZN | unknown | unknown | n/a |
1:11:GLU:OE2 | 2:3:ZN:ZN | unknown | unknown | n/a |
1:77:HIS:NE2 | 2:1:ZN:ZN | unknown | unknown | n/a |
1:107:HIS:NE2 | 2:1:ZN:ZN | unknown | unknown | n/a |
1:100:HIS:NE2 | 2:2:ZN:ZN | unknown | unknown | n/a |
1:73:ASP:OD1 | 2:1:ZN:ZN | unknown | unknown | n/a |
1:11:GLU:OE1 | 2:3:ZN:ZN | unknown | unknown | n/a |
1:104:GLU:OE2 | 2:2:ZN:ZN | unknown | unknown | n/a |
1:74:GLU:OE2 | 2:3:ZN:ZN | unknown | unknown | n/a |
1:103:ASP:OD2 | 2:1:ZN:ZN | unknown | unknown | n/a |
1:74:GLU:OE1 | 2:2:ZN:ZN | unknown | unknown | n/a |
1:104:GLU:OE1 | 2:3:ZN:ZN | unknown | unknown | n/a |
1:103:ASP:OD1 | 2:1:ZN:ZN | unknown | unknown | n/a |
1:44:GLU:OE1 | 2:2:ZN:ZN | unknown | unknown | n/a |
1:73:ASP:OD2 | 2:1:ZN:ZN | unknown | unknown | n/a |
1:74:GLU:OE1 | 2:3:ZN:ZN | unknown | unknown | n/a |
1:74:GLU:OE2 | 2:2:ZN:ZN | unknown | unknown | n/a |
Non-standard residues
Chain_ID | Seq_ID | Comp_ID | Chem_comp_name | Experimental evidences |
---|---|---|---|---|
B | 1 | ZN | ZINC ION | Distance restraints |
B | 2 | ZN | ZINC ION | None |
B | 3 | ZN | ZINC ION | None |
Sequence alignments
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 MDELRELLKAEQQGIKILKEVLKKAKEGDEQELARLNQEIVKAEKQGVKVYKEAAEKARNPEKRQVIDKILEDEEKHIEWHKAASKQGNAEQFASLVQQH |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| MDELRELLKAEQQGIKILKEVLKKAKEGDEQELARLNQEIVKAEKQGVKVYKEAAEKARNPEKRQVIDKILEDEEKHIEWHKAASKQGNAEQFASLVQQH -------110----- LQDEQRHVEEIEKKN ||||||||||||||| LQDEQRHVEEIEKKN
Chain assignments
Entity_assembly_ID (NMR) | Auth_asym_ID (model) | Length | Unmapped | Conflict | Sequence coverage (%) |
---|---|---|---|---|---|
A | A | 115 | 0 | 0 | 100.0 |
Content subtype: combined_17751_2lff.nef
Assigned chemical shifts
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 MDELRELLKAEQQGIKILKEVLKKAKEGDEQELARLNQEIVKAEKQGVKVYKEAAEKARNPEKRQVIDKILEDEEKHIEWHKAASKQGNAEQFASLVQQH | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| M.ELRELLKAEQQGIKILKEVLKKAKEGDEQELARLNQEIVKAEKQGVKVYKEAAEKARNPEKRQVIDKILEDEEKHIEWHKAASKQGNAEQFASLVQQH -------110----- LQDEQRHVEEIEKKN ||||||||||||||| LQDEQRHVEEIEKKN
Comp_index_ID | Comp_ID | Atom_ID | CS value (ppm) |
---|---|---|---|
100 | HIS | HD1 | 11.66 |
100 | HIS | ND1 | 120.5 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 763 | 744 | 97.5 |
13C chemical shifts | 529 | 404 | 76.4 |
15N chemical shifts | 136 | 125 | 91.9 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 233 | 225 | 96.6 |
13C chemical shifts | 230 | 112 | 48.7 |
15N chemical shifts | 114 | 108 | 94.7 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 530 | 519 | 97.9 |
13C chemical shifts | 299 | 292 | 97.7 |
15N chemical shifts | 22 | 17 | 77.3 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 60 | 60 | 100.0 |
13C chemical shifts | 60 | 60 | 100.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 23 | 23 | 100.0 |
13C chemical shifts | 22 | 18 | 81.8 |
15N chemical shifts | 1 | 1 | 100.0 |
Covalent bonds
Distance restraints
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 MDELRELLKAEQQGIKILKEVLKKAKEGDEQELARLNQEIVKAEKQGVKVYKEAAEKARNPEKRQVIDKILEDEEKHIEWHKAASKQGNAEQFASLVQQH | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| || |||||||||||| ...L..LLKAEQQGIKILKEVLKKAKEGDEQELARLNQEIVKAEKQGVKVYKEAAEKARNPEKRQVIDKILEDEEKHIEWHKAA.KQ.NAEQFASLVQQH -------110----- LQDEQRHVEEIEKKN ||||||||||||||| LQDEQRHVEEIEKKN
Dihedral angle restraints
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 MDELRELLKAEQQGIKILKEVLKKAKEGDEQELARLNQEIVKAEKQGVKVYKEAAEKARNPEKRQVIDKILEDEEKHIEWHKAASKQGNAEQFASLVQQH |||||||||||||||||||||||| ||||||||||||||||||||||||||| ||||||||||||||||||||||||| ||||||||||| ...LRELLKAEQQGIKILKEVLKKAKE..EQELARLNQEIVKAEKQGVKVYKEAAE....PEKRQVIDKILEDEEKHIEWHKAAS....AEQFASLVQQH --------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 -------110----- LQDEQRHVEEIEKKN ||||||||||| LQDEQRHVEEI -------110-