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Yorodumi- PDB-2w6w: Crystal structure of recombinant Sperm Whale Myoglobin under 1atm... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2w6w | ||||||
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Title | Crystal structure of recombinant Sperm Whale Myoglobin under 1atm of Xenon | ||||||
Components | MYOGLOBIN | ||||||
Keywords | OXYGEN STORAGE / HYDROPHOBIC CAVITIES / OXYGEN TRANSPORT / XENON DOCKING SITE / IRON / HEME / TRANSPORT / METAL-BINDING / MUSCLE PROTEIN | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.99 Å | ||||||
Authors | Miele, A.E. / Draghi, F. / Renzi, F. / Sciara, G. / Johnson, K.A. / Vallone, B. / Brunori, M. / Savino, C. | ||||||
Citation | Journal: Biopolymers / Year: 2009 Title: Pattern of Cavities in Globins: The Case of Human Hemoglobin. Authors: Savino, C. / Miele, A.E. / Draghi, F. / Johnson, K.A. / Sciara, G. / 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 | 2w6w.cif.gz | 54.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2w6w.ent.gz | 38.8 KB | Display | PDB format |
PDBx/mmJSON format | 2w6w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w6/2w6w ftp://data.pdbj.org/pub/pdb/validation_reports/w6/2w6w | HTTPS FTP |
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-Related structure data
Related structure data | 2w6vC 2w72C 1nazS S: Starting model for refinement C: citing same article (ref.) |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 17366.148 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PHYSETER CATODON (sperm whale) / Plasmid: PUC91 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TB-1 / References: UniProt: P02185 |
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-Non-polymers , 5 types, 166 molecules
#2: Chemical | ChemComp-HEM / | ||||||
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#3: Chemical | ChemComp-XE / #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-GOL / | #6: 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: 2.4 Å3/Da / Density % sol: 55 % / Description: NONE |
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Crystal grow | pH: 8.5 / Details: 2.6M (NH4)2SO4, 0.1M TRIS/HCL, PH8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: RIGAKU-MSC / Detector: IMAGE PLATE / Date: Apr 20, 2000 / Details: OSMIC MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→19.68 Å / Num. obs: 15044 / % possible obs: 98.1 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 7 |
Reflection shell | Resolution: 1.98→2.01 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 3.1 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1NAZ Resolution: 1.99→20 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.926 / SU B: 2.872 / SU ML: 0.083 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.162 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS WERE MODELED STEREOCHEMICA
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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: 11.53 Å2
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Refinement step | Cycle: LAST / Resolution: 1.99→20 Å
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Refine LS restraints |
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