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- PDB-6bdd: Crystal structure of Fe(II) unliganded H-NOX protein from K. algicida -
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Open data
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Basic information
Entry | Database: PDB / ID: 6bdd | ||||||
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Title | Crystal structure of Fe(II) unliganded H-NOX protein from K. algicida | ||||||
![]() | 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase | ||||||
![]() | SIGNALING PROTEIN / Nitric oxide signaling / heme nitric oxide/oxygen sensing protein | ||||||
Function / homology | Heme NO-binding / H-NOX domain superfamily / Haem-NO-binding / NO signalling/Golgi transport ligand-binding domain superfamily / heme binding / PROTOPORPHYRIN IX CONTAINING FE / 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Bruegger, J.J. / Hespen, C.W. / Marletta, M.A. | ||||||
![]() | ![]() Title: Native Alanine Substitution in the Glycine Hinge Modulates Conformational Flexibility of Heme Nitric Oxide/Oxygen (H-NOX) Sensing Proteins. Authors: Hespen, C.W. / Bruegger, J.J. / Guo, Y. / Marletta, M.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 97.9 KB | Display | ![]() |
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PDB format | ![]() | 72.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 777 KB | Display | ![]() |
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Full document | ![]() | 777.1 KB | Display | |
Data in XML | ![]() | 10.4 KB | Display | |
Data in CIF | ![]() | 14 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6bdeC ![]() 4u99S 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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Unit cell |
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Components
#1: Protein | Mass: 21284.182 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-HEM / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.04 % / Description: Rods |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M Tris-HCl, pH 8.5, 0.3 M LiCl, 34% (w/v) PEG 6000 |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 27, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→44.17 Å / Num. obs: 15750 / % possible obs: 99 % / Redundancy: 6 % / Biso Wilson estimate: 34.58 Å2 / CC1/2: 0.616 / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.78 |
Reflection shell | Resolution: 1.9→1.93 Å / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.41 / Num. unique obs: 692 / % possible all: 91.4 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4U99 Resolution: 1.901→44.17 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.88
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 114.36 Å2 / Biso mean: 42.7677 Å2 / Biso min: 19.91 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.901→44.17 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6
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Refinement TLS params. | Method: refined / Origin x: 2.795 Å / Origin y: -6.862 Å / Origin z: -2.044 Å
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Refinement TLS group |
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