+Open data
-Basic information
Entry | Database: PDB / ID: 5eui | |||||||||
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Title | Structure of predicted ancestral pika hemoglobin | |||||||||
Components |
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Keywords | OXYGEN TRANSPORT / Hemoglobin / Pika / oxygen-transport / recombinant | |||||||||
Function / homology | Function and homology information haptoglobin binding / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / peroxidase activity / oxygen binding / blood microparticle ...haptoglobin binding / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / peroxidase activity / oxygen binding / blood microparticle / iron ion binding / heme binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Ochotona princeps (American pika) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | |||||||||
Authors | Inoguchi, N. / Chandrasekhar, N. / Storz, J.F. / Moriyama, H. | |||||||||
Funding support | United States, 2items
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Citation | Journal: To Be Published Title: structure of predicted pika ancestral hemoglobin at 1.45 Angstroms resolution. Authors: Inoguchi, N. / Natarajan, C. / Storz, J.F. / Moriyama, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5eui.cif.gz | 83.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5eui.ent.gz | 60.1 KB | Display | PDB format |
PDBx/mmJSON format | 5eui.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5eui_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5eui_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5eui_validation.xml.gz | 18.7 KB | Display | |
Data in CIF | 5eui_validation.cif.gz | 28.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eu/5eui ftp://data.pdbj.org/pub/pdb/validation_reports/eu/5eui | HTTPS FTP |
-Related structure data
Related structure data | 2dn1S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 15216.353 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ochotona princeps (American pika) / Gene: HBA / Production host: Escherichia coli (E. coli) / References: UniProt: U5KQB1 | ||||
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#2: Protein | Mass: 15874.138 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ochotona princeps (American pika) / Gene: HBB / Production host: Escherichia coli (E. coli) / References: UniProt: U5KNG4 | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | This hemoglobin is the reconstructed ancestor of O. princeps and O. collaris | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.98 % |
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Crystal grow | Temperature: 299 K / Method: microbatch / pH: 8 Details: PEG 3350, sodium phosphate, potassium phosphate, calcium chloride |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9787 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 21, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→30.29 Å / Num. obs: 52380 / % possible obs: 97.94 % / Redundancy: 7 % / Rmerge(I) obs: 0.0594 / Net I/σ(I): 26.96 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2DN1 Resolution: 1.45→30.289 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.74 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→30.289 Å
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Refine LS restraints |
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LS refinement shell |
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