+Open data
-Basic information
Entry | Database: PDB / ID: 1c40 | |||||||||
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Title | BAR-HEADED GOOSE HEMOGLOBIN (AQUOMET FORM) | |||||||||
Components |
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Keywords | OXYGEN STORAGE/TRANSPORT / OXYGEN TRANSPORT / HEME / RESPIRATORY PROTEIN / ERYTHROCYTE / OXYGEN STORAGE/ TRANSPORT / OXYGEN STORAGE-TRANSPORT COMPLEX | |||||||||
Function / homology | Function and homology information hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / oxygen binding / peroxidase activity / blood microparticle ...hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / oxygen binding / peroxidase activity / 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: 2.3 Å | |||||||||
Authors | Li, S. / Liu, X. / Jing, H. / Hua, Z. / Zhang, R. / Lu, G. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: Avian haemoglobins and structural basis of high affinity for oxygen: structure of bar-headed goose aquomet haemoglobin. Authors: Liu, X.Z. / Li, S.L. / Jing, H. / Liang, Y.H. / Hua, Z.Q. / Lu, G.Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1c40.cif.gz | 72.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1c40.ent.gz | 53.8 KB | Display | PDB format |
PDBx/mmJSON format | 1c40.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1c40_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1c40_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1c40_validation.xml.gz | 14.4 KB | Display | |
Data in CIF | 1c40_validation.cif.gz | 18.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c4/1c40 ftp://data.pdbj.org/pub/pdb/validation_reports/c4/1c40 | HTTPS FTP |
-Related structure data
Related structure data | 2mhbS 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: 15360.694 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Anser indicus (Bar-headed goose) / References: UniProt: P01990 | ||
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#2: Protein | Mass: 16313.866 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Anser indicus (Bar-headed goose) / References: UniProt: P02118 | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 51.3 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.8 / Details: pH 6.80 | ||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 54 % | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 291 K / pH: 6.8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: SIEMENS X200B / Detector: AREA DETECTOR / Date: Apr 15, 1993 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→26.9 Å / Num. obs: 15772 / % possible obs: 95 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 0.1 Å2 / Rmerge(I) obs: 0.072 |
Reflection | *PLUS Redundancy: 2.66 % / Num. measured all: 28271 |
Reflection shell | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 2.41 Å / % possible obs: 70.1 % / Redundancy: 1.84 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2MHB Resolution: 2.3→26.9 Å / Rfactor Rfree error: 0.007 / Data cutoff high rms absF: 55180.99 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 29.28 Å2 / ksol: 0.29 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→26.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 26.9 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.406 / Rfactor Rwork: 0.348 |