+Open data
-Basic information
Entry | Database: PDB / ID: 2r50 | ||||||
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Title | The crystal structure of nonsymbiotic corn hemoglobin 1 | ||||||
Components | Non-symbiotic hemoglobin | ||||||
Keywords | METAL BINDING PROTEIN / corn hemoglobin / plant hemoglobin / nonsymbiotic hemoglobin / Heme / Iron / Metal-binding | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Zea mays subsp. parviglumis (Balsas teosinte) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å | ||||||
Authors | Smagghe, B.J. / Hoy, J.A. / Hargrove, M.S. | ||||||
Citation | Journal: To be Published Title: The crystal structure of nonsymbiotic corn hemoglobin 1 Authors: Smagghe, B.J. / Hoy, J.A. / Hargrove, M.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2r50.cif.gz | 146.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2r50.ent.gz | 114.5 KB | Display | PDB format |
PDBx/mmJSON format | 2r50.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2r50_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 2r50_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 2r50_validation.xml.gz | 33.9 KB | Display | |
Data in CIF | 2r50_validation.cif.gz | 47.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r5/2r50 ftp://data.pdbj.org/pub/pdb/validation_reports/r5/2r50 | HTTPS FTP |
-Related structure data
Related structure data | 1d8uS 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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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 18304.375 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zea mays subsp. parviglumis (Balsas teosinte) Species: Zea mays / Strain: subsp. parviglumis / Gene: HB, GLB1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21* DE3 / References: UniProt: Q9M593 #2: Chemical | ChemComp-HEM / #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: 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: 2.45 Å3/Da / Density % sol: 49.76 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.1M Sodium Acetate, 0.2M Ammonium Sulfate, 20% PEG MME 1900, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 23, 2004 / Details: Osmic |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→80 Å / Num. obs: 35371 / % possible obs: 99.6 % / Redundancy: 6.67 % / Biso Wilson estimate: 38.8 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 19.3 |
Reflection shell | Resolution: 2.2→2.26 Å / Redundancy: 5.24 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 6.4 / Num. unique all: 2504 / % possible all: 97.6 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1D8U Resolution: 2.2→79.06 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.922 / SU B: 6.762 / SU ML: 0.166 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.28 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.837 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→79.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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