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TitleSpectroscopically Validated pH-dependent MSOX Movies Provide Detailed Mechanism of Copper Nitrite Reductases.
Journal, issue, pagesJ. Mol. Biol., Vol. 436, Page 168706-168706, Year 2024
Publish dateNov 29, 2023 (structure data deposition date)
AuthorsRose, S.L. / Ferroni, F.M. / Horrell, S. / Brondino, C.D. / Eady, R.R. / Jaho, S. / Hough, M.A. / Owen, R.L. / Antonyuk, S.V. / Hasnain, S.S.
External linksJ. Mol. Biol. / PubMed:39002715
MethodsX-ray diffraction
Resolution1.05 - 2.18 Å
Structure data

PDB-8r8s:
Low pH (5.5) as-isolated MSOX movie series dataset 1 of the copper nitrite reductase (NirK) from Bradyrhizobium japonicum USDA110 [0.57 MGy]
Method: X-RAY DIFFRACTION / Resolution: 1.11 Å

PDB-8rfl:
Low pH (5.5) nitrite-bound MSOX movie series dataset 1 of the copper nitrite reductase (NirK) from Bradyrhizobium japonicum USDA110 [0.61 MGy] - nitrite (start)
Method: X-RAY DIFFRACTION / Resolution: 1.16 Å

PDB-8rfo:
Low pH (pH 5.5) nitrite-bound MSOX movie series dataset 2 of the copper nitrite reductase (NirK) from Bradyrhizobium japonicum USDA110 [1.22 MGy] - nitrite intermediate
Method: X-RAY DIFFRACTION / Resolution: 1.19 Å

PDB-8rfp:
Low pH (5.5) nitrite-bound MSOX movie series dataset 3 of the copper nitrite reductase (NirK) from Bradyrhizobium japonicum USDA110 [1.83 MGy] - nitrite/NO intermediate
Method: X-RAY DIFFRACTION / Resolution: 1.23 Å

PDB-8rfq:
Low pH (5.5) nitrite-bound MSOX movie series dataset 5 of the copper nitrite reductase (NirK) from Bradyrhizobium japonicum USDA110 [3.05 MGy] - nitric oxide (NO) intermediate
Method: X-RAY DIFFRACTION / Resolution: 1.32 Å

PDB-8rfr:
Low pH (5.5) nitrite-bound MSOX movie series dataset 7 of the copper nitrite reductase (NirK) from Bradyrhizobium japonicum USDA110 [4.27 MGy] - NO/water intermediate
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-8rfs:
Low pH (5.5) nitrite-bound MSOX movie series dataset 11 of the copper nitrite reductase (NirK) from Bradyrhizobium japonicum USDA110 [6.71 MGy] - water ligand
Method: X-RAY DIFFRACTION / Resolution: 1.54 Å

PDB-8rft:
Low pH (5.5) nitrite-bound MSOX movie series dataset 17 of the copper nitrite reductase (NirK) from Bradyrhizobium japonicum USDA110 [10.37 MGy] - water ligand + decarboxylated AspCAT
Method: X-RAY DIFFRACTION / Resolution: 1.7 Å

PDB-8rfu:
Low pH (5.5) nitrite-bound MSOX movie series dataset 40 of the copper nitrite reductase (NirK) from Bradyrhizobium japonicum USDA110 [24.4 MGy] - water ligand + decarboxylated AspCAT (final)
Method: X-RAY DIFFRACTION / Resolution: 2.18 Å

PDB-8rfv:
High pH (8.0) as-isolated MSOX movie series dataset 1 of the copper nitrite reductase from Bradyrhizobium sp. ORS375 (two-domain) [0.41 MGy]
Method: X-RAY DIFFRACTION / Resolution: 1.31 Å

PDB-8rfw:
High pH (8.0) as-isolated MSOX movie series dataset 2 of the copper nitrite reductase from Bradyrhizobium sp. ORS375 (two-domain) [0.82 MGy]
Method: X-RAY DIFFRACTION / Resolution: 1.33 Å

PDB-8rfx:
High pH (8.0) as-isolated MSOX movie series dataset 5 of the copper nitrite reductase from Bradyrhizobium sp. ORS375 (two-domain) [2.05 MGy]
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-8rfy:
High pH (8.0) as-isolated MSOX movie series dataset 30 of the copper nitrite reductase from Bradyrhizobium sp. ORS375 (two-domain) [12.3 MGy]
Method: X-RAY DIFFRACTION / Resolution: 1.79 Å

PDB-8rg8:
High pH (8.0) nitrite-bound MSOX movie series dataset 1 of the copper nitrite reductase from Bradyrhizobium sp. ORS375 (two-domain) [0.68 MGy]
Method: X-RAY DIFFRACTION / Resolution: 1.21 Å

PDB-8rg9:
High pH (8.0) nitrite-bound MSOX movie series dataset 2 of the copper nitrite reductase from Bradyrhizobium sp. ORS375 (two-domain) [1.36 MGy]
Method: X-RAY DIFFRACTION / Resolution: 1.25 Å

PDB-8rgb:
High pH (8.0) nitrite-bound MSOX movie series dataset 5 of the copper nitrite reductase from Bradyrhizobium sp. ORS375 (two-domain) [3.4 MGy]
Method: X-RAY DIFFRACTION / Resolution: 1.39 Å

PDB-8rgc:
High pH (8.0) nitrite-bound MSOX movie series dataset 10 of the copper nitrite reductase from Bradyrhizobium sp. ORS375 (two-domain) [6.8 MGy]
Method: X-RAY DIFFRACTION / Resolution: 1.55 Å

PDB-8rgd:
High pH (8.0) nitrite-bound MSOX movie series dataset 15 of the copper nitrite reductase from Bradyrhizobium sp. ORS375 (two-domain) [10.2 MGy]
Method: X-RAY DIFFRACTION / Resolution: 1.71 Å

PDB-8ru9:
High pH (8.0) nitrite-bound MSOX movie series dataset 1 of the copper nitrite reductase (NirK) from Bradyrhizobium japonicum USDA110 [0.69 MGy]
Method: X-RAY DIFFRACTION / Resolution: 1.1 Å

PDB-8rur:
High pH (8.0) nitrite-bound MSOX movie series dataset 2 of the copper nitrite reductase (NirK) from Bradyrhizobium japonicum USDA110 [1.38 MGy]
Method: X-RAY DIFFRACTION / Resolution: 1.13 Å

PDB-8ryj:
High pH (8.0) nitrite-bound MSOX movie series dataset 3 of the copper nitrite reductase (NirK) from Bradyrhizobium japonicum USDA110 [2.07 MGy]
Method: X-RAY DIFFRACTION / Resolution: 1.16 Å

PDB-8ryr:
High pH (8.0) nitrite-bound MSOX movie series dataset 4 of the copper nitrite reductase (NirK) from Bradyrhizobium japonicum USDA110 [2.76 MGy]
Method: X-RAY DIFFRACTION / Resolution: 1.25 Å

PDB-8ryu:
High pH (8.0) nitrite-bound MSOX movie series dataset 10 of the copper nitrite reductase (NirK) from Bradyrhizobium japonicum USDA110 [6.9 MGy]
Method: X-RAY DIFFRACTION / Resolution: 1.45 Å

PDB-8ryv:
MSOX movie series dataset 10 (11.5 MGy) for nitrite bound BrJNiR (Cu containing nitrite reductase (NirK) from Bradyrhizobium japonicum USDA110 at pH 8.
Method: X-RAY DIFFRACTION / Resolution: 1.45 Å

PDB-8s0w:
High pH (8.0) as-isolated MSOX movie series dataset 1 of the copper nitrite reductase (NirK) from Bradyrhizobium japonicum USDA110 [0.35 MGy]
Method: X-RAY DIFFRACTION / Resolution: 1.05 Å

PDB-8s2q:
High pH (8.0) as-isolated MSOX movie series dataset 2 of the copper nitrite reductase (NirK) from Bradyrhizobium japonicum USDA110 [0.7 MGy]
Method: X-RAY DIFFRACTION / Resolution: 1.05 Å

PDB-8s5x:
High pH (8.0) as-isolated MSOX movie series dataset 10 of the copper nitrite reductase (NirK) from Bradyrhizobium japonicum USDA110 [3.5 MGy]
Method: X-RAY DIFFRACTION / Resolution: 1.12 Å

PDB-8s5y:
High pH (8.0) as-isolated MSOX movie series dataset 40 of the copper nitrite reductase (NirK) from Bradyrhizobium japonicum USDA110 [14 MGy]
Method: X-RAY DIFFRACTION / Resolution: 1.3 Å

PDB-8s63:
Low pH (5.5) as-isolated MSOX movie series dataset 3 of the copper nitrite reductase (NirK) from Bradyrhizobium japonicum USDA110 [1.71 MGy]
Method: X-RAY DIFFRACTION / Resolution: 1.17 Å

PDB-8s64:
Low pH (5.5) as-isolated MSOX movie series dataset 10 of the copper nitrite reductase (NirK) from Bradyrhizobium japonicum USDA110 [5.7 MGy]
Method: X-RAY DIFFRACTION / Resolution: 1.42 Å

PDB-8s68:
Low pH (5.5) as-isolated MSOX movie series dataset 20 of the copper nitrite reductase (NirK) from Bradyrhizobium japonicum USDA110 [11.4 MGy]
Method: X-RAY DIFFRACTION / Resolution: 1.66 Å

PDB-8s69:
Low pH (5.5) as-isolated MSOX movie series dataset 40 of the copper nitrite reductase (NirK) from Bradyrhizobium japonicum USDA110 [22.8 MGy]
Method: X-RAY DIFFRACTION / Resolution: 1.78 Å

PDB-9evm:
High pH (8.0) nitrite-bound MSOX movie series dataset 30 of the copper nitrite reductase (NirK) from Bradyrhizobium japonicum USDA110 [20.7 MGy]
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

Chemicals

ChemComp-CU:
COPPER (II) ION

ChemComp-SO4:
SULFATE ION

ChemComp-HOH:
WATER

ChemComp-NO2:
NITRITE ION

ChemComp-NO:
NITRIC OXIDE

ChemComp-EPE:
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / pH buffer*YM

ChemComp-GOL:
GLYCEROL

ChemComp-CO2:
CARBON DIOXIDE

ChemComp-GLC:
alpha-D-glucopyranose

ChemComp-FRU:
beta-D-fructofuranose

Source
  • bradyrhizobium diazoefficiens usda 110 (bacteria)
  • bradyrhizobium sp. ors 375 (bacteria)
  • bradyrhizobium sp. (bacteria)
KeywordsOXIDOREDUCTASE / electron transfer / Copper nitrite reductase / Copper-containing nitrite reductase / BrJNiR / low pH / nitrite-bound / MSOX / Br2DNiR / high pH / as-isolated / resting state / Nitrite binding / nitrite reductase

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