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- PDB-3zbm: Structure of M92A variant of three-domain heme-Cu nitrite reducta... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3zbm | |||||||||
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Title | Structure of M92A variant of three-domain heme-Cu nitrite reductase from Ralstonia pickettii | |||||||||
![]() | 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 | ![]() | 116.6 KB | Display | ![]() |
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PDB format | ![]() | 88.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 826 KB | Display | ![]() |
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Full document | ![]() | 828.5 KB | Display | |
Data in XML | ![]() | 23.7 KB | Display | |
Data in CIF | ![]() | 36.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2yqbC ![]() 3ziyC ![]() 4ax3C ![]() 4aww C: citing same article ( S: Starting model for refinement |
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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: 49888.395 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: 2.78 Å3/Da / Density % sol: 56 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 20MM MES PH 6.5 20% PEG3350, 0.2 SODIUM CITRATE, 200 MM NACL, PROTEIN CONCENTRATION 7.5 MG/ML |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 11, 2012 / Details: MIRRORS |
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→32 Å / Num. obs: 43074 / % possible obs: 98.9 % / Redundancy: 5 % / Biso Wilson estimate: 22.6 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 1.87→1.92 Å / Redundancy: 3 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 1.8 / % possible all: 88.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4AWW ![]() 4aww Resolution: 1.87→40.14 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.334 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1-3 AND 460-467 ARE NOT VISIBLE IN THE ELECTRON DENSITY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.508 Å2
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Refinement step | Cycle: LAST / Resolution: 1.87→40.14 Å
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Refine LS restraints |
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