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Yorodumi- PDB-1naz: structure of microgravity-grown oxidized myoglobin mutant YQR (ISS8A) -
+Open data
-Basic information
Entry | Database: PDB / ID: 1naz | ||||||
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Title | structure of microgravity-grown oxidized myoglobin mutant YQR (ISS8A) | ||||||
Components | Myoglobin | ||||||
Keywords | oxygen storage/transport / globin fold / nearly-atomic resolution / microgravity / oxygen storage-transport COMPLEX | ||||||
Function / homology | Function and homology information hydrogen peroxide mediated signaling pathway / oxygen carrier activity / oxygen binding / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Physeter catodon (sperm whale) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.04 Å | ||||||
Authors | Miele, A.E. / Federici, L. / Sciara, G. / Draghi, F. / Brunori, M. / Vallone, B. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2003 Title: Analysis of the effect of microgravity on protein crystal quality: the case of a myoglobin triple mutant. Authors: Miele, A.E. / Federici, L. / Sciara, G. / Draghi, F. / Brunori, M. / Vallone, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1naz.cif.gz | 55.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1naz.ent.gz | 38.3 KB | Display | PDB format |
PDBx/mmJSON format | 1naz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/na/1naz ftp://data.pdbj.org/pub/pdb/validation_reports/na/1naz | HTTPS FTP |
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-Related structure data
Related structure data | 1n9fC 1n9hC 1n9iC 1n9xC 1f65S C: citing same article (ref.) 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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Details | the protein is a monomer |
-Components
#1: Protein | Mass: 17461.250 Da / Num. of mol.: 1 / Mutation: L29Y, H64Q, T67R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Physeter catodon (sperm whale) / Gene: myoglobin / Plasmid: pUC19 modified / Production host: Escherichia coli (E. coli) / Strain (production host): TB-1 / References: UniProt: P02185 | ||||
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#2: Chemical | ChemComp-OH / | ||||
#3: Chemical | #4: Chemical | ChemComp-HEM / | #5: 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: 3.03 Å3/Da / Density % sol: 59.38 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.7 Details: ammonium sulfate, tris, EDTA, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||
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: ELETTRA / Beamline: 5.2R / Wavelength: 1.001 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 2, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.001 Å / Relative weight: 1 |
Reflection | Resolution: 1.04→20 Å / Num. obs: 99221 / % possible obs: 99.8 % / Observed criterion σ(I): 1 / Redundancy: 5.31 % / Biso Wilson estimate: 8.874 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 22.4 |
Reflection shell | Resolution: 1.04→1.07 Å / Redundancy: 3.24 % / Rmerge(I) obs: 0.154 / Mean I/σ(I) obs: 18.5 / % possible all: 100 |
Reflection | *PLUS Num. obs: 97313 / Rmerge(I) obs: 0.03 |
Reflection shell | *PLUS % possible obs: 100 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb code 1f65 Resolution: 1.04→20 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 9.54 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.04→20 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor Rwork: 0.132 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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