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Yorodumi- PDB-2z68: Crystal Structure Of An Artificial Metalloprotein: Cr[N-salicylid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2z68 | ||||||
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Title | Crystal Structure Of An Artificial Metalloprotein: Cr[N-salicylidene-4-amino-3-hydroxyhydrocinnamic acid]/Wild Type Heme oxygenase | ||||||
Components | Heme oxygenase | ||||||
Keywords | OXIDOREDUCTASE / Electron-Transfer / Artificial Metalloprotein / Heme oxygenase / salophen | ||||||
Function / homology | Function and homology information heme oxygenase (biliverdin-producing) / heme oxidation / heme oxygenase (decyclizing) activity / heme catabolic process / response to oxidative stress / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Corynebacterium diphtheriae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å | ||||||
Authors | Yokoi, N. / Unno, M. / Ueno, T. / Ikeda-Saito, M. / Watanabe, Y. | ||||||
Citation | Journal: To be Published Title: Ligand design for improvement of thermal stabilityof metal complex/protein hybrids Authors: Yokoi, N. / Ueno, T. / Unno, M. / Matsui, T. / Ikeda-Saito, M. / Watanabe, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2z68.cif.gz | 184.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2z68.ent.gz | 146.2 KB | Display | PDB format |
PDBx/mmJSON format | 2z68.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z6/2z68 ftp://data.pdbj.org/pub/pdb/validation_reports/z6/2z68 | HTTPS FTP |
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-Related structure data
Related structure data | 1wzdS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 24170.158 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corynebacterium diphtheriae (bacteria) / Plasmid: pMW172-A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(de3) References: UniProt: Q54AI1, heme oxygenase (biliverdin-producing) #2: Chemical | #3: Chemical | #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: 2.05 Å3/Da / Density % sol: 40.07 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M MES pH6.5, 0.2mM Ammonium sulfate, 30% w/w PEG 2000 methyl mono ester, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 180 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 18, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→50 Å / Num. obs: 53304 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.061 / Rsym value: 0.052 / Net I/σ(I): 23.2 |
Reflection shell | Resolution: 1.58→1.64 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1WZD Resolution: 1.58→29.77 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.974 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.099 / 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: 19.755 Å2
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Refinement step | Cycle: LAST / Resolution: 1.58→29.77 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.583→1.624 Å / Total num. of bins used: 20
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