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Yorodumi- PDB-5g3g: Preserving MEtallic Sites Affected by Radiation Damage the CuT2 c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5g3g | ||||||
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Title | Preserving MEtallic Sites Affected by Radiation Damage the CuT2 case in Thermus Thermophilus multicopper Oxidase | ||||||
Components | THERMUS THERMOPHILUS MULTICOPPER OXIDASE | ||||||
Keywords | OXIDOREDUCTASE / MULTICOPPER OXIDAS / RADIATION DAMAGE / METALIC SITES / MACROMOLECULES CRYSTALLOGRAPHY / RADICAL SCAVENGERS | ||||||
Function / homology | Function and homology information hydroquinone:oxygen oxidoreductase activity / laccase / ferroxidase activity / outer membrane-bounded periplasmic space / copper ion binding Similarity search - Function | ||||||
Biological species | THERMUS THERMOPHILUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å | ||||||
Authors | Ruiz-Arellano, R. / Diaz, A. / Rosas, E. / Rudino, E. | ||||||
Citation | Journal: To be Published Title: Preserving Metallic Sites Affected by Radiation Damage the Cut2 Case in Thermus Thermophilus Multicopper Oxidase Authors: Ruiz-Arellano, R. / Diaz, A. / Rosas, E. / Stojanoff, V. / Rudino, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5g3g.cif.gz | 121.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5g3g.ent.gz | 93.9 KB | Display | PDB format |
PDBx/mmJSON format | 5g3g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5g3g_validation.pdf.gz | 457.4 KB | Display | wwPDB validaton report |
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Full document | 5g3g_full_validation.pdf.gz | 461.7 KB | Display | |
Data in XML | 5g3g_validation.xml.gz | 22.3 KB | Display | |
Data in CIF | 5g3g_validation.cif.gz | 33.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g3/5g3g ftp://data.pdbj.org/pub/pdb/validation_reports/g3/5g3g | HTTPS FTP |
-Related structure data
Related structure data | 5g3bC 5g3cC 5g3dC 5g3eC 5g3fC 5g3hC 2yaeS 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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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 48791.457 Da / Num. of mol.: 1 / Fragment: RESIDUES 24-462 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / References: UniProt: I7AL37 |
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-Non-polymers , 5 types, 384 molecules
#2: Chemical | #3: Chemical | ChemComp-MPD / ( #4: Chemical | ChemComp-MRD / ( #5: Chemical | ChemComp-NA / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.89 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9793 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→19.72 Å / Num. obs: 45713 / % possible obs: 98.3 % / Observed criterion σ(I): 17.17 / Redundancy: 6.3 % / Biso Wilson estimate: 12.92 Å2 / Rmerge(I) obs: 0.09 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.59 / % possible all: 96.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2YAE Resolution: 1.84→19.707 Å / SU ML: 0.16 / σ(F): 1.35 / Phase error: 16.07 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.84→19.707 Å
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Refine LS restraints |
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LS refinement shell |
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