Solution structure of the Family 1 carbohydrate-binding module Y5A mutant with mannosylated Ser3
ID | Type | Value order | Atom ID 1 | Atom ID 2 |
---|---|---|---|---|
1 | disulfide | sing | 1:CYS8:SG | 1:CYS25:SG |
2 | disulfide | sing | 1:CYS19:SG | 1:CYS35:SG |
3 | ether | sing | 1:SER3:OG | 2:MAN1:C1 |
Polymer type: polypeptide(L)
Total | 1H | 13C | 15N | |
---|---|---|---|---|
All | 90.1 % (329 of 365) | 99.5 % (184 of 185) | 75.9 % (107 of 141) | 97.4 % (38 of 39) |
Backbone | 83.0 % (176 of 212) | 98.7 % (75 of 76) | 66.7 % (68 of 102) | 97.1 % (33 of 34) |
Sidechain | 100.0 % (183 of 183) | 100.0 % (109 of 109) | 100.0 % (69 of 69) | 100.0 % (5 of 5) |
Aromatic | 100.0 % (28 of 28) | 100.0 % (14 of 14) | 100.0 % (14 of 14) | |
Methyl | 100.0 % (32 of 32) | 100.0 % (16 of 16) | 100.0 % (16 of 16) |
1. Exoglucanase 1
TQSHAGQCGG IGYSGPTVCA SGTTCQVLNP YYSQCLSolvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5, Details 5 mg/mL CBM-Y5A, 50 mM [U-2H] sodium acetate, 0.1 mg/mL DSS, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | CBM-Y5A | natural abundance | protein | 5 mg/mL |
2 | DSS | natural abundance | 0.1 mg/mL | |
3 | sodium acetate | [U-2H] | buffer | 50 mM |
4 | H2O | natural abundance | solvent | 90 % |
5 | D2O | [U-2H] | solvent | 10 % |
Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 5, Details 5 mg/mL CBM-Y5A, 50 mM [U-2H] sodium acetate, 0.1 mg/mL DSS, 100% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
6 | CBM-Y5A | natural abundance | protein | 5 mg/mL |
7 | DSS | natural abundance | 0.1 mg/mL | |
8 | sodium acetate | [U-2H] | 50 mM | |
9 | D2O | [U-2H] | solvent | 100 % |
Bruker AvanceIII - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5, Details 5 mg/mL CBM-Y5A, 50 mM [U-2H] sodium acetate, 0.1 mg/mL DSS, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | CBM-Y5A | natural abundance | protein | 5 mg/mL |
2 | DSS | natural abundance | 0.1 mg/mL | |
3 | sodium acetate | [U-2H] | buffer | 50 mM |
4 | H2O | natural abundance | solvent | 90 % |
5 | D2O | [U-2H] | solvent | 10 % |
Bruker AvanceIII - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5, Details 5 mg/mL CBM-Y5A, 50 mM [U-2H] sodium acetate, 0.1 mg/mL DSS, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | CBM-Y5A | natural abundance | protein | 5 mg/mL |
2 | DSS | natural abundance | 0.1 mg/mL | |
3 | sodium acetate | [U-2H] | buffer | 50 mM |
4 | H2O | natural abundance | solvent | 90 % |
5 | D2O | [U-2H] | solvent | 10 % |
Bruker AvanceIII - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5, Details 5 mg/mL CBM-Y5A, 50 mM [U-2H] sodium acetate, 0.1 mg/mL DSS, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | CBM-Y5A | natural abundance | protein | 5 mg/mL |
2 | DSS | natural abundance | 0.1 mg/mL | |
3 | sodium acetate | [U-2H] | buffer | 50 mM |
4 | H2O | natural abundance | solvent | 90 % |
5 | D2O | [U-2H] | solvent | 10 % |
Bruker AvanceIII - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5, Details 5 mg/mL CBM-Y5A, 50 mM [U-2H] sodium acetate, 0.1 mg/mL DSS, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | CBM-Y5A | natural abundance | protein | 5 mg/mL |
2 | DSS | natural abundance | 0.1 mg/mL | |
3 | sodium acetate | [U-2H] | buffer | 50 mM |
4 | H2O | natural abundance | solvent | 90 % |
5 | D2O | [U-2H] | solvent | 10 % |
Bruker AvanceIII - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5, Details 5 mg/mL CBM-Y5A, 50 mM [U-2H] sodium acetate, 0.1 mg/mL DSS, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | CBM-Y5A | natural abundance | protein | 5 mg/mL |
2 | DSS | natural abundance | 0.1 mg/mL | |
3 | sodium acetate | [U-2H] | buffer | 50 mM |
4 | H2O | natural abundance | solvent | 90 % |
5 | D2O | [U-2H] | solvent | 10 % |
Bruker AvanceIII - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5, Details 5 mg/mL CBM-Y5A, 50 mM [U-2H] sodium acetate, 0.1 mg/mL DSS, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | CBM-Y5A | natural abundance | protein | 5 mg/mL |
2 | DSS | natural abundance | 0.1 mg/mL | |
3 | sodium acetate | [U-2H] | buffer | 50 mM |
4 | H2O | natural abundance | solvent | 90 % |
5 | D2O | [U-2H] | solvent | 10 % |
Bruker AvanceIII - 600 MHz
State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 5, Details 5 mg/mL CBM-Y5A, 50 mM [U-2H] sodium acetate, 0.1 mg/mL DSS, 100% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
6 | CBM-Y5A | natural abundance | protein | 5 mg/mL |
7 | DSS | natural abundance | 0.1 mg/mL | |
8 | sodium acetate | [U-2H] | 50 mM | |
9 | D2O | [U-2H] | solvent | 100 % |
Bruker AvanceIII - 600 MHz
State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 5, Details 5 mg/mL CBM-Y5A, 50 mM [U-2H] sodium acetate, 0.1 mg/mL DSS, 100% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
6 | CBM-Y5A | natural abundance | protein | 5 mg/mL |
7 | DSS | natural abundance | 0.1 mg/mL | |
8 | sodium acetate | [U-2H] | 50 mM | |
9 | D2O | [U-2H] | solvent | 100 % |
Bruker AvanceIII - 600 MHz
State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 5, Details 5 mg/mL CBM-Y5A, 50 mM [U-2H] sodium acetate, 0.1 mg/mL DSS, 100% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
6 | CBM-Y5A | natural abundance | protein | 5 mg/mL |
7 | DSS | natural abundance | 0.1 mg/mL | |
8 | sodium acetate | [U-2H] | 50 mM | |
9 | D2O | [U-2H] | solvent | 100 % |
Bruker AvanceIII - 600 MHz
State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 5, Details 5 mg/mL CBM-Y5A, 50 mM [U-2H] sodium acetate, 0.1 mg/mL DSS, 100% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
6 | CBM-Y5A | natural abundance | protein | 5 mg/mL |
7 | DSS | natural abundance | 0.1 mg/mL | |
8 | sodium acetate | [U-2H] | 50 mM | |
9 | D2O | [U-2H] | solvent | 100 % |
Bruker AvanceIII - 600 MHz
State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 5, Details 5 mg/mL CBM-Y5A, 50 mM [U-2H] sodium acetate, 0.1 mg/mL DSS, 100% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
6 | CBM-Y5A | natural abundance | protein | 5 mg/mL |
7 | DSS | natural abundance | 0.1 mg/mL | |
8 | sodium acetate | [U-2H] | 50 mM | |
9 | D2O | [U-2H] | solvent | 100 % |
Bruker AvanceIII - 600 MHz
State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 5, Details 5 mg/mL CBM-Y5A, 50 mM [U-2H] sodium acetate, 0.1 mg/mL DSS, 100% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
6 | CBM-Y5A | natural abundance | protein | 5 mg/mL |
7 | DSS | natural abundance | 0.1 mg/mL | |
8 | sodium acetate | [U-2H] | 50 mM | |
9 | D2O | [U-2H] | solvent | 100 % |
Properties
Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints | combined_36056_5x3c.nef |
Input source #2: Coordindates | 5x3c.cif |
Diamagnetism of the molecular assembly | True (excluding Oxygen atoms) |
Whether the assembly has a disulfide bond | True (see coordinates for details) |
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
Ptnr_site_1 | Ptnr_site_2 | Redox_state_prediction_1 | Redox_state_prediction_2 | Distance (Å) |
---|---|---|---|---|
A:8:CYS:SG | A:25:CYS:SG | oxidized, CA 55.373, CB 46.68 ppm | oxidized, CA 56.18, CB 39.1 ppm | 2.021 |
A:19:CYS:SG | A:35:CYS:SG | oxidized, CA 54.09, CB 39.62 ppm | oxidized, CA 54.05, CB 38.2 ppm | 2.031 |
Other 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 (Å) |
---|---|---|---|---|
1:3:SER:OG | 2:1:MAN:C1 | unknown | unknown | n/a |
Non-standard residues
Chain_ID | Seq_ID | Comp_ID | Chem_comp_name | Experimental evidences |
---|---|---|---|---|
B | 1 | MAN | alpha-D-mannopyranose | Assigned chemical shifts, Distance restraints |
Sequence alignments
--------10--------20--------30------ TQSHAGQCGGIGYSGPTVCASGTTCQVLNPYYSQCL |||||||||||||||||||||||||||||||||||| TQSHAGQCGGIGYSGPTVCASGTTCQVLNPYYSQCL
Chain assignments
Entity_assembly_ID (NMR) | Auth_asym_ID (model) | Length | Unmapped | Conflict | Sequence coverage (%) |
---|---|---|---|---|---|
A | A | 36 | 0 | 0 | 100.0 |
Content subtype: combined_36056_5x3c.nef
Assigned chemical shifts
--------10--------20--------30------ TQSHAGQCGGIGYSGPTVCASGTTCQVLNPYYSQCL |||||||||||||||||||||||||||||||||||| TQSHAGQCGGIGYSGPTVCASGTTCQVLNPYYSQCL
- X | X
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 185 | 184 | 99.5 |
13C chemical shifts | 141 | 105 | 74.5 |
15N chemical shifts | 39 | 38 | 97.4 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 76 | 75 | 98.7 |
13C chemical shifts | 72 | 36 | 50.0 |
15N chemical shifts | 34 | 33 | 97.1 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 109 | 109 | 100.0 |
13C chemical shifts | 69 | 69 | 100.0 |
15N chemical shifts | 5 | 5 | 100.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 16 | 16 | 100.0 |
13C chemical shifts | 16 | 16 | 100.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 14 | 14 | 100.0 |
13C chemical shifts | 14 | 14 | 100.0 |
Comp_index_ID | Comp_ID |
---|---|
1 | MAN |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|
Covalent bonds
Distance restraints
--------10--------20--------30------ TQSHAGQCGGIGYSGPTVCASGTTCQVLNPYYSQCL |||||||||||||||||||||||||||||||||||| TQSHAGQCGGIGYSGPTVCASGTTCQVLNPYYSQCL
- X | X
Dihedral angle restraints
--------10--------20--------30------ TQSHAGQCGGIGYSGPTVCASGTTCQVLNPYYSQCL ||| ||||||||| |||||||||||||||||||| ..SHA.QCGGIGYSG.TVCASGTTCQVLNPYYSQCL