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Yorodumi- PDB-1hv4: CRYSTAL STRUCTURE ANALYSIS OF BAR-HEAD GOOSE HEMOGLOBIN (DEOXY FORM) -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hv4 | ||||||
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Title | CRYSTAL STRUCTURE ANALYSIS OF BAR-HEAD GOOSE HEMOGLOBIN (DEOXY FORM) | ||||||
Components |
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Keywords | OXYGEN STORAGE/TRANSPORT / ALLOSTERIC MECHANISM / OXYGEN TRANSPORT / HEME / RESPIRATORY PROTEIN / OXYGEN STORAGE-TRANSPORT COMPLEX | ||||||
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 | Anser indicus (Bar-headed goose) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Liang, Y. / Hua, Z. / Liang, X. / Xu, Q. / Lu, G. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: The crystal structure of bar-headed goose hemoglobin in deoxy form: the allosteric mechanism of a hemoglobin species with high oxygen affinity. Authors: Liang, Y. / Hua, Z. / Liang, X. / Xu, Q. / Lu, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hv4.cif.gz | 234.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hv4.ent.gz | 192.2 KB | Display | PDB format |
PDBx/mmJSON format | 1hv4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hv/1hv4 ftp://data.pdbj.org/pub/pdb/validation_reports/hv/1hv4 | HTTPS FTP |
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-Related structure data
Related structure data | 1a4fS 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: 15361.679 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Anser indicus (Bar-headed goose) / Cell: ERYTHROCYTES / Cellular location: CYTOPLASM / Tissue: BLOOD / References: UniProt: P01990 #2: Protein | Mass: 16313.866 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Anser indicus (Bar-headed goose) / Cell: ERYTHROCYTES / Cellular location: CYTOPLASM / Tissue: BLOOD / References: UniProt: P02118 #3: Chemical | ChemComp-HEM / |
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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: 2.67 Å3/Da / Density % sol: 53.99 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: PEG 6000, potassium phosphate , pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 291 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: SIEMENS X200 / Detector: AREA DETECTOR / Date: May 10, 1995 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.57→36.89 Å / Num. all: 45509 / Num. obs: 30654 / % possible obs: 67.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 1.9 % / Biso Wilson estimate: 28.4 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 2.57→2.73 Å / Redundancy: 1.14 % / Rmerge(I) obs: 0.146 / Mean I/σ(I) obs: 4.4 / Num. unique all: 1779 / % possible all: 24 |
Reflection | *PLUS Num. measured all: 57884 / Rmerge(I) obs: 0.0541 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1A4F Resolution: 2.8→36.89 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 63263.6 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 30.63 Å2 / ksol: 0.299 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→36.89 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | |||||||||||||||||||||||||
LS refinement shell | Resolution: 2.8→2.98 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: CNS / Version: 1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 10.1 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 27.7 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.329 / % reflection Rfree: 10.6 % / Rfactor Rwork: 0.285 |