+Open data
-Basic information
Entry | Database: PDB / ID: 1i3d | ||||||
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Title | HUMAN CARBONMONOXY HEMOGLOBIN BART'S (GAMMA4) | ||||||
Components | HEMOGLOBIN GAMMA CHAINS | ||||||
Keywords | OXYGEN STORAGE/TRANSPORT / OXYGEN TRANSPORT / OXYGEN STORAGE-TRANSPORT COMPLEX | ||||||
Function / homology | Function and homology information cellular oxidant detoxification / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / oxygen transport / hydrogen peroxide catabolic process / oxygen carrier activity / carbon dioxide transport / oxygen binding ...cellular oxidant detoxification / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / oxygen transport / hydrogen peroxide catabolic process / oxygen carrier activity / carbon dioxide transport / oxygen binding / Factors involved in megakaryocyte development and platelet production / heme binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Kidd, R.D. / Baker, H.M. / Mathews, A.J. / Brittain, T. / Baker, E.N. | ||||||
Citation | Journal: Protein Sci. / Year: 2001 Title: Oligomerization and ligand binding in a homotetrameric hemoglobin: two high-resolution crystal structures of hemoglobin Bart's (gamma(4)), a marker for alpha-thalassemia. Authors: Kidd, R.D. / Baker, H.M. / Mathews, A.J. / Brittain, T. / Baker, E.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1i3d.cif.gz | 81.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1i3d.ent.gz | 59.9 KB | Display | PDB format |
PDBx/mmJSON format | 1i3d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1i3d_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1i3d_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1i3d_validation.xml.gz | 21.7 KB | Display | |
Data in CIF | 1i3d_validation.cif.gz | 29.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i3/1i3d ftp://data.pdbj.org/pub/pdb/validation_reports/i3/1i3d | HTTPS FTP |
-Related structure data
Related structure data | 1i3eC 1cbmS C: citing same article (ref.) 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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Details | The second globin dimer of the homotetramer is generated by the two fold axis: -x, -y+1, z. |
-Components
#1: Protein | Mass: 16031.255 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HBG1 / Plasmid: PRMAE389 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): GSY112 / References: UniProt: P69891 #2: Chemical | #3: Chemical | #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: 2.1 Å3/Da / Density % sol: 41.4 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.9 Details: acetic acid/KOH, MePEG 5000, pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / pH: 7 | ||||||||||||||||||||||||||||||
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: BL7-1 / Wavelength: 1.08 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 10, 1998 / Details: mirror |
Radiation | Monochromator: Cyclindrically bent triangular Si(111) asymmetric cut, horizontal focus Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. all: 27848 / Num. obs: 27848 / % possible obs: 91.5 % / Observed criterion σ(F): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.283 / Mean I/σ(I) obs: 3 / Num. unique all: 2942 / % possible all: 98.5 |
Reflection | *PLUS Num. measured all: 105161 |
Reflection shell | *PLUS % possible obs: 98.5 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1CBM Resolution: 1.7→20 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 32.1634 Å2 / ksol: 0.310647 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.211 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 16.9 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.376 / % reflection Rfree: 9.8 % / Rfactor Rwork: 0.332 |