+Open data
-Basic information
Entry | Database: PDB / ID: 5ker | ||||||
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Title | Deer mouse recombinant hemoglobin from high altitude species | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / oxygen-transport | ||||||
Function / homology | Function and homology information hemoglobin complex / oxygen carrier activity / oxygen binding / iron ion binding / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Peromyscus maniculatus (North American deer mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.202 Å | ||||||
Authors | Inoguchi, N. / Natarajan, C. / Storz, J.F. / Moriyama, H. | ||||||
Citation | Journal: PLoS ONE / Year: 2017 Title: Alteration of the alpha 1 beta 2/ alpha 2 beta 1 subunit interface contributes to the increased hemoglobin-oxygen affinity of high-altitude deer mice. Authors: Inoguchi, N. / Mizuno, N. / Baba, S. / Kumasaka, T. / 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 | 5ker.cif.gz | 242.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ker.ent.gz | 199.6 KB | Display | PDB format |
PDBx/mmJSON format | 5ker.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ker_validation.pdf.gz | 2.9 MB | Display | wwPDB validaton report |
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Full document | 5ker_full_validation.pdf.gz | 2.9 MB | Display | |
Data in XML | 5ker_validation.xml.gz | 52.4 KB | Display | |
Data in CIF | 5ker_validation.cif.gz | 71.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ke/5ker ftp://data.pdbj.org/pub/pdb/validation_reports/ke/5ker | HTTPS FTP |
-Related structure data
Related structure data | 4h2lS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 14893.987 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Peromyscus maniculatus (North American deer mouse) Gene: HBA, Hba, HBAT1 / Production host: Escherichia coli (E. coli) / References: UniProt: A4ZQ87 #2: Protein | Mass: 15786.198 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Peromyscus maniculatus (North American deer mouse) Gene: HBB, HBB-T1, HBB-T2 / Production host: Escherichia coli (E. coli) / References: UniProt: B7SBL4 #3: Chemical | ChemComp-HEM / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.86 % |
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Crystal grow | Temperature: 299 K / Method: vapor diffusion, hanging drop Details: 26% (w/v) PEG 3350 in 50 mM sodium/potassium phosphate, pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 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: Jul 18, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→29.56 Å / Num. obs: 65478 / % possible obs: 71 % / Redundancy: 1.6 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 9.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4H2L Resolution: 2.202→29.56 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.56 / Phase error: 21.27 / 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: 2.202→29.56 Å
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Refine LS restraints |
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LS refinement shell |
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