+Open data
-Basic information
Entry | Database: PDB / ID: 1d8u | ||||||
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Title | CRYSTAL STRUCTURE OF NON-SYMBIOTIC PLANT HEMOGLOBIN FROM RICE | ||||||
Components | NON-SYMBIOTIC HEMOGLOBIN | ||||||
Keywords | OXYGEN STORAGE/TRANSPORT / GLOBIN / BIS-HISTIDYL / HEME PROTEIN / OXYGEN STORAGE-TRANSPORT complex | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on other nitrogenous compounds as donors; With a cytochrome as acceptor / response to nitrite / response to nitrate / response to nitric oxide / oxygen binding / oxidoreductase activity / heme binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Oryza sativa (Asian cultivated rice) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.35 Å | ||||||
Authors | Hargrove, M. / Brucker, E.A. / Stec, B. / Olson, J.S. / Phillips Jr., G.N. | ||||||
Citation | Journal: Structure Fold.Des. / Year: 2000 Title: Crystal structure of a nonsymbiotic plant hemoglobin. Authors: Hargrove, M.S. / Brucker, E.A. / Stec, B. / Sarath, G. / Arredondo-Peter, R. / Klucas, R.V. / Olson, J.S. / Phillips Jr., G.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1d8u.cif.gz | 83.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d8u.ent.gz | 63.6 KB | Display | PDB format |
PDBx/mmJSON format | 1d8u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1d8u_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1d8u_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1d8u_validation.xml.gz | 18.6 KB | Display | |
Data in CIF | 1d8u_validation.cif.gz | 25.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d8/1d8u ftp://data.pdbj.org/pub/pdb/validation_reports/d8/1d8u | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 18469.432 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryza sativa (Asian cultivated rice) / Organ: ROOT / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / References: UniProt: O04986 #2: Chemical | #3: 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: 3.49 Å3/Da / Density % sol: 64.71 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: AMMONIUM PHOSPHATE, SUCROSE, POTASSIUM PHOSPHATE, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 22K | |||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.74 |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Aug 21, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.74 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 19025 / % possible obs: 87.8 % / Observed criterion σ(I): 0 / Redundancy: 8.06 % / Biso Wilson estimate: 27.2 Å2 / Rmerge(I) obs: 0.7 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 2.35→2.42 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.271 / % possible all: 0.7 |
Reflection | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 50 Å / Num. obs: 21422 / % possible obs: 80 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.69 |
Reflection shell | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 2.4 Å / % possible obs: 46 % / Num. unique obs: 1634 / Rmerge(I) obs: 0.223 / Mean I/σ(I) obs: 2.3 |
-Processing
Software |
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Refinement | Resolution: 2.35→50 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.35→50 Å
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Refine LS restraints |
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Software | *PLUS Name: 'XPLOR 3.1 AND CNS' / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.208 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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