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Open data
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Basic information
Entry | Database: PDB / ID: 7zos | |||||||||
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Title | Class 1 Phytoglobin from Sugar beet (BvPgb1.2) | |||||||||
![]() | Non-symbiotic hemoglobin class 1 | |||||||||
![]() | OXYGEN BINDING / Plant Hemoglobin / Phytoglobin / Nitrogen Metabolism / Redox balance | |||||||||
Function / homology | ![]() oxygen carrier activity / oxygen binding / heme binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Nyblom, M. / Christensen, S. / Eriksson, N. / Bulow, L. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Oxidative Implications of Substituting a Conserved Cysteine Residue in Sugar Beet Phytoglobin BvPgb 1.2. Authors: Christensen, S. / Groth, L. / Leiva-Eriksson, N. / Nyblom, M. / Bulow, L. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 56.3 KB | Display | ![]() |
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PDB format | ![]() | 31.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 838 KB | Display | ![]() |
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Full document | ![]() | 839.9 KB | Display | |
Data in XML | ![]() | 9 KB | Display | |
Data in CIF | ![]() | 11.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7z1uC ![]() 3zhwS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 19253.303 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: Chemical | ChemComp-CYN / |
#4: Chemical | ChemComp-FC6 / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.75 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 20% (w/v) PEG6000, 0.1 M Citrate, pH 5.0 |
-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: Sep 27, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→68.413 Å / Num. obs: 18443 / % possible obs: 100 % / Redundancy: 25.6 % / Biso Wilson estimate: 38.56 Å2 / CC1/2: 0.999 / Net I/σ(I): 23.7 |
Reflection shell | Resolution: 1.901→1.934 Å / Num. unique obs: 907 / CC1/2: 0.727 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3zhw Resolution: 1.9→47.9 Å / SU ML: 0.1629 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.2442 / Stereochemistry target values: CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.94 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→47.9 Å
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Refine LS restraints |
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LS refinement shell |
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