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Yorodumi- PDB-4f69: Carbonmonoxy structure of Tyr11Phe/Gln44Leu/Thr48Val/Ala55Trp Cer... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4f69 | ||||||
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Title | Carbonmonoxy structure of Tyr11Phe/Gln44Leu/Thr48Val/Ala55Trp Cerebratulus lacteus mini-hemoglobin | ||||||
Components | Neural hemoglobin | ||||||
Keywords | OXYGEN TRANSPORT / oxygen-storage / apolar tunnel | ||||||
Function / homology | Function and homology information oxygen carrier activity / oxygen binding / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Cerebratulus lacteus (milky ribbon-worm) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.6 Å | ||||||
Authors | Soman, J. / Salter, M.D. / Olson, J.S. | ||||||
Citation | Journal: To be Published Title: Carbonmonoxy structure of Tyr11Phe/Gln44Leu/Thr48Val/Ala55Trp Cerebratulus lacteus mini-hemoglobin Authors: Soman, J. / Salter, M.D. / Olson, J.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4f69.cif.gz | 38.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4f69.ent.gz | 25.2 KB | Display | PDB format |
PDBx/mmJSON format | 4f69.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4f69_validation.pdf.gz | 798.1 KB | Display | wwPDB validaton report |
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Full document | 4f69_full_validation.pdf.gz | 799.4 KB | Display | |
Data in XML | 4f69_validation.xml.gz | 8.5 KB | Display | |
Data in CIF | 4f69_validation.cif.gz | 11.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f6/4f69 ftp://data.pdbj.org/pub/pdb/validation_reports/f6/4f69 | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 11629.138 Da / Num. of mol.: 1 / Mutation: Tyr11Phe/Gln44Leu/Thr48Val/Ala55Trp Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cerebratulus lacteus (milky ribbon-worm) Production host: Escherichia coli (E. coli) / References: UniProt: O76242 |
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#2: Chemical | ChemComp-CMO / |
#3: Chemical | ChemComp-GOL / |
#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: 2.37 Å3/Da / Density % sol: 48 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.4 Details: Protein crystallized from 2.5 mM Ammonium Sulfate and 0.1M sodium Citrate, pH 5.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5412 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5412 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.6→27.08 Å / Num. obs: 14641 / % possible obs: 97 % / Redundancy: 2.62 % / Rmerge(I) obs: 0.048 / Χ2: 0.99 / Net I/σ(I): 11.7 / Scaling rejects: 290 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.6→27.076 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.845 / SU ML: 0.63 / σ(F): 1.42 / Phase error: 21.74 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.372 Å2 / ksol: 0.394 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 64.47 Å2 / Biso mean: 23.9547 Å2 / Biso min: 13.1 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→27.076 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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