Solution structure of the Ni metallochaperone HypA from Helicobacter pylori
MHEYSVVSSL IALCEEHAKK NQAHKIERVV VGIGERSAMD KSLFVSAFET FREESLVCKD AILDIVDEKV ELECKDCSHV FKPNALDYGV CEKCHSKNVI ITQGNEMRLL SLEMLAE
ID | Type | Value order | Atom ID 1 | Atom ID 2 |
---|---|---|---|---|
1 | disulfide | sing | 1:CYS74:SG | 2:ZN1:ZN |
2 | disulfide | sing | 1:CYS77:SG | 2:ZN1:ZN |
3 | disulfide | sing | 1:CYS91:SG | 2:ZN1:ZN |
4 | disulfide | sing | 1:CYS94:SG | 2:ZN1:ZN |
Polymer type: polypeptide(L)
Total | 1H | 13C | 15N | |
---|---|---|---|---|
All | 95.4 % (1291 of 1353) | 94.3 % (661 of 701) | 97.4 % (516 of 530) | 93.4 % (114 of 122) |
Backbone | 97.9 % (685 of 700) | 97.0 % (230 of 237) | 98.3 % (341 of 347) | 98.3 % (114 of 116) |
Sidechain | 93.5 % (716 of 766) | 92.9 % (431 of 464) | 96.3 % (285 of 296) | 0.0 % (0 of 6) |
Aromatic | 85.5 % (65 of 76) | 86.8 % (33 of 38) | 84.2 % (32 of 38) | |
Methyl | 100.0 % (140 of 140) | 100.0 % (70 of 70) | 100.0 % (70 of 70) |
1. entity 1
MHEYSVVSSL IALCEEHAKK NQAHKIERVV VGIGERSAMD KSLFVSAFET FREESLVCKD AILDIVDEKV ELECKDCSHV FKPNALDYGV CEKCHSKNVI ITQGNEMRLL SLEMLAESolvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2, Details 1 mM [U-13C; U-15N] HypA, 20 mM HEPES, 200 mM sodium chloride, 1 mM TCEP, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | HypA | [U-13C; U-15N] | 1 mM | |
2 | HEPES | natural abundance | 20 mM | |
3 | sodium chloride | natural abundance | 200 mM | |
4 | TCEP | natural abundance | 1 mM |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | internal | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | internal | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | internal | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | internal | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | internal | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | internal | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | internal | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | internal | indirect | 0.1013291 |
Bruker Avance - 900 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2, Details 1 mM [U-13C; U-15N] HypA, 20 mM HEPES, 200 mM sodium chloride, 1 mM TCEP, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | HypA | [U-13C; U-15N] | 1 mM | |
2 | HEPES | natural abundance | 20 mM | |
3 | sodium chloride | natural abundance | 200 mM | |
4 | TCEP | natural abundance | 1 mM |
Bruker Avance - 900 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2, Details 1 mM [U-13C; U-15N] HypA, 20 mM HEPES, 200 mM sodium chloride, 1 mM TCEP, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | HypA | [U-13C; U-15N] | 1 mM | |
2 | HEPES | natural abundance | 20 mM | |
3 | sodium chloride | natural abundance | 200 mM | |
4 | TCEP | natural abundance | 1 mM |
Bruker Avance - 900 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2, Details 1 mM [U-13C; U-15N] HypA, 20 mM HEPES, 200 mM sodium chloride, 1 mM TCEP, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | HypA | [U-13C; U-15N] | 1 mM | |
2 | HEPES | natural abundance | 20 mM | |
3 | sodium chloride | natural abundance | 200 mM | |
4 | TCEP | natural abundance | 1 mM |
Bruker Avance - 900 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2, Details 1 mM [U-13C; U-15N] HypA, 20 mM HEPES, 200 mM sodium chloride, 1 mM TCEP, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | HypA | [U-13C; U-15N] | 1 mM | |
2 | HEPES | natural abundance | 20 mM | |
3 | sodium chloride | natural abundance | 200 mM | |
4 | TCEP | natural abundance | 1 mM |
Bruker Avance - 900 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2, Details 1 mM [U-13C; U-15N] HypA, 20 mM HEPES, 200 mM sodium chloride, 1 mM TCEP, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | HypA | [U-13C; U-15N] | 1 mM | |
2 | HEPES | natural abundance | 20 mM | |
3 | sodium chloride | natural abundance | 200 mM | |
4 | TCEP | natural abundance | 1 mM |
Bruker Avance - 900 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2, Details 1 mM [U-13C; U-15N] HypA, 20 mM HEPES, 200 mM sodium chloride, 1 mM TCEP, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | HypA | [U-13C; U-15N] | 1 mM | |
2 | HEPES | natural abundance | 20 mM | |
3 | sodium chloride | natural abundance | 200 mM | |
4 | TCEP | natural abundance | 1 mM |
Bruker Avance - 900 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2, Details 1 mM [U-13C; U-15N] HypA, 20 mM HEPES, 200 mM sodium chloride, 1 mM TCEP, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | HypA | [U-13C; U-15N] | 1 mM | |
2 | HEPES | natural abundance | 20 mM | |
3 | sodium chloride | natural abundance | 200 mM | |
4 | TCEP | natural abundance | 1 mM |
Bruker Avance - 900 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2, Details 1 mM [U-13C; U-15N] HypA, 20 mM HEPES, 200 mM sodium chloride, 1 mM TCEP, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | HypA | [U-13C; U-15N] | 1 mM | |
2 | HEPES | natural abundance | 20 mM | |
3 | sodium chloride | natural abundance | 200 mM | |
4 | TCEP | natural abundance | 1 mM |
Agilent DDR2 - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2, Details 1 mM [U-13C; U-15N] HypA, 20 mM HEPES, 200 mM sodium chloride, 1 mM TCEP, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | HypA | [U-13C; U-15N] | 1 mM | |
2 | HEPES | natural abundance | 20 mM | |
3 | sodium chloride | natural abundance | 200 mM | |
4 | TCEP | natural abundance | 1 mM |
Agilent DDR2 - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2, Details 1 mM [U-13C; U-15N] HypA, 20 mM HEPES, 200 mM sodium chloride, 1 mM TCEP, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | HypA | [U-13C; U-15N] | 1 mM | |
2 | HEPES | natural abundance | 20 mM | |
3 | sodium chloride | natural abundance | 200 mM | |
4 | TCEP | natural abundance | 1 mM |
Agilent DDR2 - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2, Details 1 mM [U-13C; U-15N] HypA, 20 mM HEPES, 200 mM sodium chloride, 1 mM TCEP, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | HypA | [U-13C; U-15N] | 1 mM | |
2 | HEPES | natural abundance | 20 mM | |
3 | sodium chloride | natural abundance | 200 mM | |
4 | TCEP | natural abundance | 1 mM |
Agilent DDR2 - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2, Details 1 mM [U-13C; U-15N] HypA, 20 mM HEPES, 200 mM sodium chloride, 1 mM TCEP, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | HypA | [U-13C; U-15N] | 1 mM | |
2 | HEPES | natural abundance | 20 mM | |
3 | sodium chloride | natural abundance | 200 mM | |
4 | TCEP | natural abundance | 1 mM |
Agilent DDR2 - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2, Details 1 mM [U-13C; U-15N] HypA, 20 mM HEPES, 200 mM sodium chloride, 1 mM TCEP, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | HypA | [U-13C; U-15N] | 1 mM | |
2 | HEPES | natural abundance | 20 mM | |
3 | sodium chloride | natural abundance | 200 mM | |
4 | TCEP | natural abundance | 1 mM |
Agilent DDR2 - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2, Details 1 mM [U-13C; U-15N] HypA, 20 mM HEPES, 200 mM sodium chloride, 1 mM TCEP, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | HypA | [U-13C; U-15N] | 1 mM | |
2 | HEPES | natural abundance | 20 mM | |
3 | sodium chloride | natural abundance | 200 mM | |
4 | TCEP | natural abundance | 1 mM |
Agilent DDR2 - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2, Details 1 mM [U-13C; U-15N] HypA, 20 mM HEPES, 200 mM sodium chloride, 1 mM TCEP, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | HypA | [U-13C; U-15N] | 1 mM | |
2 | HEPES | natural abundance | 20 mM | |
3 | sodium chloride | natural abundance | 200 mM | |
4 | TCEP | natural abundance | 1 mM |
Agilent DDR2 - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2, Details 1 mM [U-13C; U-15N] HypA, 20 mM HEPES, 200 mM sodium chloride, 1 mM TCEP, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | HypA | [U-13C; U-15N] | 1 mM | |
2 | HEPES | natural abundance | 20 mM | |
3 | sodium chloride | natural abundance | 200 mM | |
4 | TCEP | natural abundance | 1 mM |
Agilent DDR2 - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2, Details 1 mM [U-13C; U-15N] HypA, 20 mM HEPES, 200 mM sodium chloride, 1 mM TCEP, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | HypA | [U-13C; U-15N] | 1 mM | |
2 | HEPES | natural abundance | 20 mM | |
3 | sodium chloride | natural abundance | 200 mM | |
4 | TCEP | natural abundance | 1 mM |
Agilent DDR2 - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2, Details 1 mM [U-13C; U-15N] HypA, 20 mM HEPES, 200 mM sodium chloride, 1 mM TCEP, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | HypA | [U-13C; U-15N] | 1 mM | |
2 | HEPES | natural abundance | 20 mM | |
3 | sodium chloride | natural abundance | 200 mM | |
4 | TCEP | natural abundance | 1 mM |
Properties
Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints | combined_34257_6g81.nef |
Input source #2: Coordindates | 6g81.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…) |
---|---|---|---|---|
1:74:CYS:SG | 2:1:ZN:ZN | unknown | unknown | n/a |
1:77:CYS:SG | 2:1:ZN:ZN | unknown | unknown | n/a |
1:91:CYS:SG | 2:1:ZN:ZN | unknown | unknown | n/a |
1:94:CYS:SG | 2:1: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 | None |
Sequence alignments
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 MHEYSVVSSLIALCEEHAKKNQAHKIERVVVGIGERSAMDKSLFVSAFETFREESLVCKDAILDIVDEKVELECKDCSHVFKPNALDYGVCEKCHSKNVI |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| MHEYSVVSSLIALCEEHAKKNQAHKIERVVVGIGERSAMDKSLFVSAFETFREESLVCKDAILDIVDEKVELECKDCSHVFKPNALDYGVCEKCHSKNVI -------110------- ITQGNEMRLLSLEMLAE ||||||||||||||||| ITQGNEMRLLSLEMLAE
Chain assignments
Entity_assembly_ID (NMR) | Auth_asym_ID (model) | Length | Unmapped | Conflict | Sequence coverage (%) |
---|---|---|---|---|---|
A | A | 117 | 0 | 0 | 100.0 |
Content subtype: combined_34257_6g81.nef
Assigned chemical shifts
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 MHEYSVVSSLIALCEEHAKKNQAHKIERVVVGIGERSAMDKSLFVSAFETFREESLVCKDAILDIVDEKVELECKDCSHVFKPNALDYGVCEKCHSKNVI |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| MHEYSVVSSLIALCEEHAKKNQAHKIERVVVGIGERSAMDKSLFVSAFETFREESLVCKDAILDIVDEKVELECKDCSHVFKPNALDYGVCEKCHSKNVI -------110------- ITQGNEMRLLSLEMLAE ||||||||||||||||| ITQGNEMRLLSLEMLAE
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 701 | 665 | 94.9 |
13C chemical shifts | 530 | 516 | 97.4 |
15N chemical shifts | 126 | 114 | 90.5 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 237 | 233 | 98.3 |
13C chemical shifts | 234 | 231 | 98.7 |
15N chemical shifts | 116 | 114 | 98.3 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 464 | 432 | 93.1 |
13C chemical shifts | 296 | 285 | 96.3 |
15N chemical shifts | 10 | 0 | 0.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 74 | 74 | 100.0 |
13C chemical shifts | 74 | 74 | 100.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 38 | 32 | 84.2 |
13C chemical shifts | 38 | 32 | 84.2 |
Covalent bonds
Distance restraints
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 MHEYSVVSSLIALCEEHAKKNQAHKIERVVVGIGERSAMDKSLFVSAFETFREESLVCKDAILDIVDEKVELECKDCSHVFKPNALDYGVCEKCHSKNVI |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| MHEYSVVSSLIALCEEHAKKNQAHKIERVVVGIGERSAMDKSLFVSAFETFREESLVCKDAILDIVDEKVELECKDCSHVFKPNALDYGVCEKCHSKNVI -------110------- ITQGNEMRLLSLEMLAE ||||||||||||||||| ITQGNEMRLLSLEMLAE
Dihedral angle restraints
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 MHEYSVVSSLIALCEEHAKKNQAHKIERVVVGIGERSAMDKSLFVSAFETFREESLVCKDAILDIVDEKVELECKDCSHVFKPNALDYGVCEKCHSKNVI |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||| |||||||| MHEYSVVSSLIALCEEHAKKNQAHKIERVVVGIGERSAMDKSLFVSAFETFREESLVCKDAILDIVDEKVELECKDCSHVFKPN...YGVC.KCHSKNVI -------110------- ITQGNEMRLLSLEMLAE ||||||||||||||||| ITQGNEMRLLSLEMLAE