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Yorodumi- PDB-4c44: Crystal Structure of Truncated Plant Hemoglobin from Arabidopsis ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4c44 | ||||||
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Title | Crystal Structure of Truncated Plant Hemoglobin from Arabidopsis thaliana | ||||||
Components | 2-ON-2 HEMOGLOBIN | ||||||
Keywords | OXYGEN BINDING | ||||||
Function / homology | Function and homology information response to auxin / oxygen transport / oxygen carrier activity / oxygen binding / response to hypoxia / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | ARABIDOPSIS THALIANA (thale cress) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | ||||||
Authors | Mukhi, N. / Dhindwal, S. / Kumar, P. / Kaur, J. / Kundu, S. | ||||||
Citation | Journal: To be Published Title: X-Ray Crystallographic Structural Characteristics of Truncated Hemoglobin from Arabidopsis Thaliana Authors: Mukhi, N. / Dhindwal, S. / Kumar, P. / Kaur, J. / Kundu, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4c44.cif.gz | 47.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4c44.ent.gz | 32.9 KB | Display | PDB format |
PDBx/mmJSON format | 4c44.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c4/4c44 ftp://data.pdbj.org/pub/pdb/validation_reports/c4/4c44 | HTTPS FTP |
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-Related structure data
Related structure data | 1ngkS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 20223.594 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q67XG0 |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-NA / |
#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: 4.09 Å3/Da / Density % sol: 69.98 % / Description: NONE |
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Crystal grow | Details: 1.2M SODIUM POTASSIUM TARTARATE TETRAHYDRATE, 0.1M TRIS PH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.5418 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 12, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→50 Å / Num. obs: 9881 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 5.68 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.24 |
Reflection shell | Resolution: 2.65→2.7 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1NGK Resolution: 2.65→43.2 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.903 / SU B: 8.427 / SU ML: 0.176 / Cross valid method: THROUGHOUT / ESU R: 0.322 / ESU R Free: 0.259 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.82 Å2
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Refinement step | Cycle: LAST / Resolution: 2.65→43.2 Å
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Refine LS restraints |
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