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- PDB-3ziy: Structure of three-domain heme-Cu nitrite reductase from Ralstoni... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3ziy | |||||||||
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Title | Structure of three-domain heme-Cu nitrite reductase from Ralstonia pickettii at 1.01 A resolution | |||||||||
![]() | COPPER-CONTAINING NITRITE REDUCTASE | |||||||||
![]() | OXIDOREDUCTASE / ELECTRON TRANSFER / PROTON CHANNEL / DENITRIFICATION | |||||||||
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. / Han, C. / Eady, R.R. / Hasnain, S.S. | |||||||||
![]() | ![]() Title: Structures of protein-protein complexes involved in electron transfer. Authors: Antonyuk, S.V. / Han, C. / Eady, R.R. / Hasnain, S.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 | ![]() | 414.6 KB | Display | ![]() |
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PDB format | ![]() | 342.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 808.2 KB | Display | ![]() |
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Full document | ![]() | 817.3 KB | Display | |
Data in XML | ![]() | 29.1 KB | Display | |
Data in CIF | ![]() | 47.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2yqbC ![]() 3zbmC ![]() 4ax3C ![]() 2z00S 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 49948.516 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: E2STD2, UniProt: B2UHR8*PLUS, nitrite reductase (NO-forming) | ||||
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#2: Chemical | #3: Chemical | ChemComp-HEC / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50 % / Description: NONE |
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Crystal grow | pH: 6.5 / Details: PEG, SODIUM CITRITE, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 4, 2012 / Details: MIRRORS |
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.01→40 Å / Num. obs: 277728 / % possible obs: 100 % / Redundancy: 4.3 % / Biso Wilson estimate: 6.4 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 18 |
Reflection shell | Resolution: 1.01→1.05 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2Z00 Resolution: 1.01→37.76 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.984 / SU B: 0.437 / SU ML: 0.01 / Cross valid method: THROUGHOUT / ESU R: 0.016 / ESU R Free: 0.017 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
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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: 12.6 Å2
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Refinement step | Cycle: LAST / Resolution: 1.01→37.76 Å
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Refine LS restraints |
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