+Open data
-Basic information
Entry | Database: PDB / ID: 1hbr | ||||||
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Title | R-STATE FORM OF CHICKEN HEMOGLOBIN D | ||||||
Components | (PROTEIN (HEMOGLOBIN D)) x 2 | ||||||
Keywords | OXYGEN STORAGE/TRANSPORT / HEMOGLOBIN D (R-STATE) 1 / HEMOGLOBIN / AVIAN / HIGH COOPERATIITY / OXYGEN TRANSPORT / OXYGEN STORAGE-TRANSPORT COMPLEX | ||||||
Function / homology | Function and homology information Erythrocytes take up carbon dioxide and release oxygen / Erythrocytes take up oxygen and release carbon dioxide / Scavenging of heme from plasma / haptoglobin-hemoglobin complex / organic acid binding / cellular oxidant detoxification / hemoglobin binding / hemoglobin complex / hydrogen peroxide catabolic process / Neutrophil degranulation ...Erythrocytes take up carbon dioxide and release oxygen / Erythrocytes take up oxygen and release carbon dioxide / Scavenging of heme from plasma / haptoglobin-hemoglobin complex / organic acid binding / cellular oxidant detoxification / hemoglobin binding / hemoglobin complex / hydrogen peroxide catabolic process / Neutrophil degranulation / oxygen carrier activity / oxygen binding / iron ion binding / heme binding / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Knapp, E. / Oliveira, M.A. / Xie, Q. / Ernst, S.R. / Riggs, A.F. / Hackert, M.L. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1999 Title: The structural and functional analysis of the hemoglobin D component from chicken. Authors: Knapp, J.E. / Oliveira, M.A. / Xie, Q. / Ernst, S.R. / Riggs, A.F. / Hackert, M.L. #1: Journal: J.Mol.Biol. / Year: 1983 Title: Structure of Human Oxyhaemoglobin at 2.1 A Resolution Authors: Shaanan, B. #2: Journal: J.Biol.Chem. / Year: 1983 Title: The Nucleotide Sequence of the Adult Chicken Alpha-Globin Genes Authors: Dodgson, J.B. / Engel, J.D. #3: Journal: J.Biol.Chem. / Year: 1983 Title: Analysis of the Adult Chicken Beta-Globin Gene Authors: Dolan, M. / Dodgson, J.B. / Engel, J.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hbr.cif.gz | 128.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hbr.ent.gz | 100 KB | Display | PDB format |
PDBx/mmJSON format | 1hbr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hb/1hbr ftp://data.pdbj.org/pub/pdb/validation_reports/hb/1hbr | HTTPS FTP |
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-Related structure data
Related structure data | 1hhoS 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.883125, -0.046056, 0.466871), Vector: |
-Components
#1: Protein | Mass: 15715.911 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Cell: ERYTHROCYTES / Cellular location: CYTOPLASM / Tissue: BLOOD / References: UniProt: P02001 #2: Protein | Mass: 16357.919 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Cell: ERYTHROCYTES / Cellular location: CYTOPLASM / Tissue: BLOOD / References: UniProt: P02112 #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: 2.6 Å3/Da / Density % sol: 52.7 % | |||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: pH 7.0 | |||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: unknown | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: SDMS / Detector: AREA DETECTOR / Date: Mar 1, 1994 / Details: NO MIRRORS |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→10 Å / Num. obs: 29702 / % possible obs: 99.1 % / Redundancy: 9.6 % / Biso Wilson estimate: 28 Å2 / Rsym value: 8.1 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 2.3→2.5 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.3 / Rsym value: 23.9 / % possible all: 97.7 |
Reflection | *PLUS Redundancy: 6.8 % / Rmerge(I) obs: 0.068 |
Reflection shell | *PLUS Rmerge(I) obs: 0.239 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HHO Resolution: 2.3→10 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 32.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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