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- PDB-6otx: Crystallographic Structure of (HbII-HbIII)-O2 from Lucina pectina... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6otx | ||||||
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Title | Crystallographic Structure of (HbII-HbIII)-O2 from Lucina pectinata at pH 7.0 | ||||||
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![]() | OXYGEN TRANSPORT / hemeprotein | ||||||
Function / homology | ![]() oxygen carrier activity / oxygen binding / response to hypoxia / heme binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Marchany-Rivera, D. / Smith, C.A. / Rodriguez-Perez, J.D. / Lopez-Garriga, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Lucina pectinata oxyhemoglobin (II-III) heterodimer pH susceptibility. Authors: Marchany-Rivera, D. / Smith, C.A. / Rodriguez-Perez, J.D. / Lopez-Garriga, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 144.5 KB | Display | ![]() |
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PDB format | ![]() | 112.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 425.4 KB | Display | ![]() |
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Full document | ![]() | 428.1 KB | Display | |
Data in XML | ![]() | 2.1 KB | Display | |
Data in CIF | ![]() | 5.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6otwC ![]() 6otyC ![]() 3pt8S 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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Unit cell |
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Components
#1: Protein | Mass: 17146.715 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||||
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#2: Protein | Mass: 17450.910 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.09 Å3/Da / Density % sol: 60.2 % |
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Crystal grow | Temperature: 293 K / Method: counter-diffusion / pH: 7 / Details: Sodium Formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 12, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.19499 Å / Relative weight: 1 |
Reflection | Resolution: 2.539→50 Å / Num. obs: 15012 / % possible obs: 99.6 % / Redundancy: 10 % / Net I/σ(I): 36.6 |
Reflection shell | Resolution: 2.54→2.58 Å / Num. unique obs: 784334 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3PT8 Resolution: 2.539→33.558 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.82
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 201.81 Å2 / Biso mean: 82.7208 Å2 / Biso min: 44.76 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.539→33.558 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5
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Refinement TLS params. | Method: refined / Origin x: -9.7797 Å / Origin y: 12.9466 Å / Origin z: 24.5872 Å
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Refinement TLS group |
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