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Yorodumi- PDB-1jeb: Chimeric Human/Mouse Carbonmonoxy Hemoglobin (Human Zeta2 / Mouse... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jeb | ||||||
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Title | Chimeric Human/Mouse Carbonmonoxy Hemoglobin (Human Zeta2 / Mouse Beta2) | ||||||
Components |
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Keywords | OXYGEN STORAGE/TRANSPORT / oxygen transport / OXYGEN STORAGE-TRANSPORT COMPLEX | ||||||
Function / homology | Function and homology information hemoglobin beta binding / regulation of eIF2 alpha phosphorylation by heme / nitric oxide transport / cellular oxidant detoxification / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / oxygen transport / hemopoiesis ...hemoglobin beta binding / regulation of eIF2 alpha phosphorylation by heme / nitric oxide transport / cellular oxidant detoxification / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / oxygen transport / hemopoiesis / erythrocyte development / hydrogen peroxide catabolic process / oxygen carrier activity / carbon dioxide transport / oxygen binding / myelin sheath / iron ion binding / heme binding / protein-containing complex binding / extracellular exosome / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Kidd, R.D. / Russell, J.E. / Watmough, N.J. / Baker, E.N. / Brittain, T. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: The role of beta chains in the control of the hemoglobin oxygen binding function: chimeric human/mouse proteins, structure, and function. Authors: Kidd, R.D. / Russell, J.E. / Watmough, N.J. / Baker, E.N. / Brittain, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jeb.cif.gz | 131 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jeb.ent.gz | 102 KB | Display | PDB format |
PDBx/mmJSON format | 1jeb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jeb_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 1jeb_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 1jeb_validation.xml.gz | 28.4 KB | Display | |
Data in CIF | 1jeb_validation.cif.gz | 37.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/je/1jeb ftp://data.pdbj.org/pub/pdb/validation_reports/je/1jeb | HTTPS FTP |
-Related structure data
Related structure data | 1bbbS 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: 15553.847 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Description: transgenic-knockout mouse expressing chimeric human zeta / mouse beta-single hemoglobin Gene: HBZ / Production host: Mus musculus (house mouse) / Strain (production host): BALB/c / References: UniProt: P02008 #2: Protein | Mass: 15639.868 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: transgenic-knockout mouse expressing chimeric human zeta / mouse beta-single hemoglobin Source: (natural) Mus musculus (house mouse) / References: UniProt: P02088 #3: Chemical | ChemComp-HEM / #4: Chemical | ChemComp-CMO / #5: 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: 2.92 Å3/Da / Density % sol: 58 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: Bicine/NaOH, MePEG 550, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / pH: 7.4 | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 1, 2001 / Details: mirror |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. all: 43348 / Num. obs: 43348 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 23.9 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 2.9 / Num. unique all: 4307 / % possible all: 100 |
Reflection | *PLUS Num. measured all: 192738 |
Reflection shell | *PLUS % possible obs: 100 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BBB Resolution: 2.1→25 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: flat model / Bsol: 39.5297 Å2 / ksol: 0.304517 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 28 Å / Num. reflection obs: 43240 / σ(F): 0 / % reflection Rfree: 10 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 40.1 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.395 / % reflection Rfree: 10.5 % / Rfactor Rwork: 0.379 |