novel manganese-containing cupin TM1459
Thermotoga maritima
State in the Current Structure
| Assembly | Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Associated Components | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|
| 1 | Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count | Chain A； UniProt 1–114 Chain B； UniProt 1–114 | Not recorded | MN MANGANESE (II) ION × 2 UNL UNKNOWN LIGAND × 1 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION,SITTING DROP,NANODROP；pH 5.2；293 K；50% (v/v) PEG-200, 0.1M Phosphate-citrate pH 4.2 0.2M NaCl, pH 5.2, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K | Resolution 1.65 Å R-free 0.249 |
Other States of the Same Protein in the Database
Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.
| Other PDB | Difference from Current Entry 1VJ2 | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 5WSD Crystal structure of a cupin protein (tm1459) in apo form Deposited 2016-12-06 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1–114（114 aa）
Chain B
1–114（114 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；25% Jeffamine ED-2001, 0.1M MES
|
Resolution 1.20 Å R-free 0.201 |
| 5WSE Crystal structure of a cupin protein (tm1459) in osmium (Os) substituted form I Deposited 2016-12-06 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1–114（114 aa）
Chain D
1–114（114 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | OS OSMIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；25% w/v polyethylene glycol 1500, 0.1M MES
|
Resolution 1.12 Å R-free 0.180 |
| 5WSE Crystal structure of a cupin protein (tm1459) in osmium (Os) substituted form I Deposited 2016-12-06 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain B
1–114（114 aa）
Chain C
1–114（114 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | OS OSMIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；25% w/v polyethylene glycol 1500, 0.1M MES
|
Resolution 1.12 Å R-free 0.180 |
| 5WSF Crystal structure of a cupin protein (tm1459) in osmium (Os)-substituted form II Deposited 2016-12-06 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1–114（114 aa）
Chain D
1–114（114 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | OS OSMIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；25% w/v polyethylene glycol 1500, 0.1M MES
|
Resolution 1.11 Å R-free 0.183 |
| 5WSF Crystal structure of a cupin protein (tm1459) in osmium (Os)-substituted form II Deposited 2016-12-06 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain B
1–114（114 aa）
Chain C
1–114（114 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | OS OSMIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；25% w/v polyethylene glycol 1500, 0.1M MES
|
Resolution 1.11 Å R-free 0.183 |
| 6L2D Crystal structure of a cupin protein (tm1459) in copper (Cu) substituted form Deposited 2019-10-03 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1–114（114 aa）
Chain B
1–114（114 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | CU COPPER (II) ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；25%(w/v) Jeffamine ED-2001, 0.1M MES
|
Resolution 1.20 Å R-free 0.186 |
| 6L2E Crystal structure of a cupin protein (tm1459, H52A mutant) in copper (Cu) substituted form Deposited 2019-10-03 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1–114（114 aa）
Chain B
1–114（114 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | CU COPPER (II) ION × 3 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；25% w/v Jeffamine ED-2001, 0.1M MES
|
Resolution 1.20 Å R-free 0.179 |
| 6L2F Crystal structure of a cupin protein (tm1459, H54AH58A mutant) in copper (Cu) substituted form Deposited 2019-10-03 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1–114（114 aa）
Chain B
1–114（114 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | CU COPPER (II) ION × 2 P33 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；25%(w/v) Jeffamine ED-2001, 0.1M MES
|
Resolution 1.23 Å R-free 0.188 |
| 8AWN Crystal structure of a manganese-containing cupin (tm1459) from Thermotoga maritima, variant C106Q Deposited 2022-08-30 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1–114（114 aa）
|
Mutation：C106Q | CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4；289 K；1 M LiCl
0.1 M citrate pH 4.0
20 % PEG6000
16 mg/ml protein concentration
|
Resolution 1.45 Å R-free 0.173 |
| 8AWO Crystal structure of a manganese-containing cupin (tm1459) from Thermotoga maritima, variant AIFQ (Y7A/M38I/Y83F/C106Q) Deposited 2022-08-30 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1–114（114 aa）
Chain B
1–114（114 aa）
|
Mutation：Y7A, M38I, Y83F, C106Q Mutation：Y7A, M38I, Y83F, C106Q | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；289 K；8 mg/ml protein concentration
0.1 M Tris pH 8.5
2 M ammonium sulfate
|
Resolution 1.70 Å R-free 0.242 |
| 8AWP Crystal structure of a manganese-containing cupin (tm1459) from Thermotoga maritima, variant 208 (V19I/R23H/M38I/I60F/C106Q) Deposited 2022-08-30 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1–114（114 aa）
Chain B
1–114（114 aa）
|
Mutation：V19I, R23H, M38I, I60F, C106Q Mutation：V19I, R23H, M38I, I60F, C106Q | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；14.2 mg/ml protein concentration
1.6M Sodium citrate tribasic dihydrate pH 6.5
|
Resolution 1.59 Å R-free 0.208 |
| 8HJX Crystal structure of a cupin protein (tm1459, H52A/H58E mutant) in copper (Cu) substituted form Deposited 2022-11-24 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1–114（114 aa）
Chain B
1–114（114 aa）
|
Mutation：H52A/H58E Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：H52A/H58E Non-standard monomer：Yes (specific site not provided by mmCIF) | CU COPPER (II) ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；25% w/v Jeffamine ED-2001, 0.1M MES pH6.0
|
Resolution 1.15 Å R-free 0.183 |
| 8HJY Crystal structure of a cupin protein (tm1459, H52A/H58E/F104W mutant) in copper (Cu) substituted form Deposited 2022-11-24 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1–114（114 aa）
Chain B
1–114（114 aa）
|
Mutation：H52A/H58E/F104W Mutation：H52A/H58E/F104W | CU COPPER (II) ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；25% w/v Jeffamine ED-2001, 0.1M MES pH 6.0
|
Resolution 1.18 Å R-free 0.191 |
| 8HJZ Crystal structure of a cupin protein (tm1459, H52A/H58Q mutant) in copper (Cu) substituted form Deposited 2022-11-24 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1–114（114 aa）
Chain B
1–114（114 aa）
|
Mutation：H52A/H58Q Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：H52A/H58Q Non-standard monomer：Yes (specific site not provided by mmCIF) | CU COPPER (II) ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；25% w/v Jeffamine ED-2001, 0.1M MES pH 6.0
|
Resolution 1.22 Å R-free 0.188 |
| 8ZYG Crystal structure of a cupin protein (tm1459, I49C-4py/H52A/C106D mutant) in copper (Cu) substituted form Deposited 2024-06-17 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1–114（114 aa）
Chain B
1–114（114 aa）
|
Mutation：I49C/H52A/C106D Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：I49C/H52A/C106D Non-standard monomer：Yes (specific site not provided by mmCIF) | P6G HEXAETHYLENE GLYCOL × 1 CU COPPER (II) ION × 2 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；26-28% w/v Jeffamine ED-2001, 0.1M MES pH6.0
|
Resolution 1.08 Å R-free 0.171 |
| 8ZYH Crystal structure of a cupin protein (tm1459, I49C-4py/H52A/H54A/C106D mutant) in copper (Cu) substituted form Deposited 2024-06-17 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1–114（114 aa）
Chain B
1–114（114 aa）
|
Mutation：I49C/H52A/H54A/C106D Mutation：I49C/H52A/H54A/C106D | P6G HEXAETHYLENE GLYCOL × 1 CU COPPER (II) ION × 3 KN6 4-THIOPYRIDINE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；26-28% w/v Jeffamine ED-2001, 0.1M MES pH6.0
|
Resolution 1.07 Å R-free 0.163 |
| 9JET Crystal structure of a cupin protein (tm1459) in manganese (Mn) substituted form Deposited 2024-09-03 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1–114（114 aa）
Chain B
1–114（114 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | MN MANGANESE (II) ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；25%(w/v) Jeffamine ED-2001, 0.1M MES
|
Resolution 1.19 Å R-free 0.201 |
| 9JEU Crystal structure of a cupin protein (tm1459) in iron (Fe) substituted form Deposited 2024-09-03 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1–114（114 aa）
Chain B
1–114（114 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | FE FE (III) ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；25%(w/v) Jeffamine ED-2001, 0.1 M MES
|
Resolution 1.19 Å R-free 0.186 |
| 9JEV Crystal structure of a cupin protein (tm1459) in zinc (Zn) substituted form Deposited 2024-09-03 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1–114（114 aa）
Chain B
1–114（114 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；25%(w/v) Jeffamine ED-2001, 0.1 M MES
|
Resolution 1.12 Å R-free 0.177 |
| 9JEW Crystal structure of a cupin protein (tm1459, C106V mutant) in iron (Fe) substituted form Deposited 2024-09-03 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1–114（114 aa）
Chain B
1–114（114 aa）
|
Mutation：C106V Mutation：C106V | FE FE (III) ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；25%(w/v) Jeffamine ED-2001, 0.1 M MES
|
Resolution 1.08 Å R-free 0.168 |
| 9XS8 Crystal structure of a cupin protein (tm1459, H52A/H54A/H92A/C106E mutant) in ruthenium(p-cymene) bound form Deposited 2025-11-20 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1–114（114 aa）
Chain B
1–114（114 aa）
|
Mutation：H52A/H54A/H92A/C106E Mutation：H52A/H54A/H92A/C106E | MML 1-methyl-4-(1-methylethyl)benzene × 1 RU RUTHENIUM ION × 2 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；25% w/v Jeffamine ED-2001, 0.1M MES
|
Resolution 1.26 Å R-free 0.198 |
| 9XS9 Crystal structure of a cupin protein (tm1459, R39K/H52A/H54A/H92A/C106E mutant) in ruthenium(p-cymene) bound form Deposited 2025-11-20 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1–114（114 aa）
Chain B
1–114（114 aa）
|
Mutation：R39K/H52A/H54A/H92A/C106E Mutation：R39K/H52A/H54A/H92A/C106E | MML 1-methyl-4-(1-methylethyl)benzene × 2 RU RUTHENIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；25% w/v Jeffamine ED-2001, 0.1M MES
|
Resolution 1.09 Å R-free 0.161 |
| 9XSA Crystal structure of a cupin protein (tm1459, R39M/H52A/H54A/H92A/C106E mutant) in ruthenium(p-cymene) bound form Deposited 2025-11-20 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1–114（114 aa）
Chain B
1–114（114 aa）
|
Mutation：R39M/H52A/H54A/H92A/C106E Mutation：R39M/H52A/H54A/H92A/C106E | MML 1-methyl-4-(1-methylethyl)benzene × 2 RU RUTHENIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；25% w/v Jeffamine ED-2001, 0.1M MES
|
Resolution 1.42 Å R-free 0.251 |
21 other PDB entries and 23 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | Q9X1H0_THEMA |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A； PDBConstruct 13–126； UniProt 1–114 Author chain B； PDBConstruct 13–126； UniProt 1–114 |