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- PDB-2yqb: Structure of P93A variant of three-domain heme-Cu nitrite reducta... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2yqb | |||||||||
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Title | Structure of P93A variant of three-domain heme-Cu nitrite reductase from Ralstonia pickettii at 1.4 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 | ![]() | 231.6 KB | Display | ![]() |
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PDB format | ![]() | 185.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3zbmC ![]() 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: 49922.477 Da / Num. of mol.: 1 / Mutation: YES 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: 7.5 Details: 20MM MES PH 6.5, 20% PEG3350, 0.2M SODIUM CITRATE, 200 MM NACL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 10, 2012 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.41→18.08 Å / Num. obs: 102529 / % possible obs: 99.9 % / Redundancy: 4.6 % / Biso Wilson estimate: 9.7 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 1.41→1.48 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.3 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4AWW ![]() 4aww Resolution: 1.41→18.07 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.626 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.045 / ESU R Free: 0.045 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 8.983 Å2
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Refinement step | Cycle: LAST / Resolution: 1.41→18.07 Å
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Refine LS restraints |
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