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- PDB-6qpv: Crystal structure of as isolated Y323A mutant of haem-Cu containi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6qpv | |||||||||
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Title | Crystal structure of as isolated Y323A mutant of haem-Cu containing nitrite reductase from Ralstonia pickettii | |||||||||
![]() | Copper-containing nitrite reductase | |||||||||
![]() | METAL BINDING PROTEIN / haem and Cu containing nitrite reductase / inter-copper electron transfer | |||||||||
Function / homology | ![]() nitrite reductase (NO-forming) / nitrite reductase (NO-forming) activity / periplasmic space / electron transfer activity / copper ion binding / heme binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Antonyuk, S.V. / Shenoy, R.T. / Hedison, T.M. / Eady, R.R. / Hasnain, S.S. / Scrutton, N.S. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Unexpected Roles of a Tether Harboring a Tyrosine Gatekeeper Residue in Modular Nitrite Reductase Catalysis. Authors: Hedison, T.M. / Shenoy, R.T. / Iorgu, A.I. / Heyes, D.J. / Fisher, K. / Wright, G.S.A. / Hay, S. / Eady, R.R. / Antonyuk, S.V. / Hasnain, S.S. / Scrutton, N.S. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 220.9 KB | Display | ![]() |
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PDB format | ![]() | 171.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6qptC ![]() 6qpuC ![]() 6qpxC ![]() 6qpzC ![]() 6qq0C ![]() 6qq1C ![]() 6qq2C ![]() 3ziyS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 49856.422 Da / Num. of mol.: 2 / Mutation: Y323A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: U3G913, UniProt: I6NAW4*PLUS, nitrite reductase (NO-forming) #2: Chemical | ChemComp-CU / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.16 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M HEPES (pH7.5), 20% PEG 3350, 0.2 M Sodium citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 2, 2018 |
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96861 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→43.83 Å / Num. obs: 169421 / % possible obs: 99.9 % / Redundancy: 4.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.068 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 4.5 % / Rmerge(I) obs: 1.227 / Mean I/σ(I) obs: 1 / Num. unique obs: 37585 / CC1/2: 0.655 / Rsym value: 0.65 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3ziy Resolution: 1.6→42.83 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.831 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.483 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→42.83 Å
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Refine LS restraints |
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