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Yorodumi- PDB-2qz7: The crystal structure of a homologue of telluride resistance prot... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qz7 | ||||||
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Title | The crystal structure of a homologue of telluride resistance protein (TerD), SCO6318 from Streptomyces coelicolor A3(2) | ||||||
Components | Uncharacterized protein SCO6318 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / APC7352 / homologue of telluride resistance protein (TerD) / SCO6318 / Streptomyces coelicolor A3(2) / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | TerD domain / TerD domain / sav2460 like domains / Lipoxygenase-1 / Sandwich / Mainly Beta / TerD domain-containing protein Function and homology information | ||||||
Biological species | Streptomyces coelicolor A3 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å | ||||||
Authors | Tan, K. / Xu, X. / Zheng, Z. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The crystal structure of a homologue of telluride resistance protein (TerD), SCO6318 from Streptomyces coelicolor A3(2). Authors: Tan, K. / Xu, X. / Zheng, Z. / Savchenko, A. / Edwards, A. / Joachimiak, A. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1, 2 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY ... BIOMOLECULE: 1, 2 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS EXPERIMENTALLY UNKNOWN, HOWEVER, FROM PACKING IT IS LIKELY A MONOMER. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qz7.cif.gz | 80 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qz7.ent.gz | 64 KB | Display | PDB format |
PDBx/mmJSON format | 2qz7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qz/2qz7 ftp://data.pdbj.org/pub/pdb/validation_reports/qz/2qz7 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | Experimentally unknown. From molecular packing, it is likely monomeric. |
-Components
#1: Protein | Mass: 21438.230 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces coelicolor A3(2) (bacteria) Species: Streptomyces coelicolorStreptomyces albidoflavus / Strain: A3(2), M145 / Gene: SCO6318, SCIF3.20c / Plasmid: p15Tv Lic / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q93RS6 #2: Chemical | ChemComp-NA / #3: Chemical | #4: 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: 2.29 Å3/Da / Density % sol: 46.32 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.6 Details: 0.1M Hepes, 3.4M Na Formate, 40% Jeffamine M-600, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 3, 2006 / Details: Mirrors |
Radiation | Monochromator: Si 111 Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97929 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→46.18 Å / Num. all: 24107 / Num. obs: 24107 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.4 % / Biso Wilson estimate: 41.3 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 45.75 |
Reflection shell | Resolution: 2.1→2.15 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.591 / Mean I/σ(I) obs: 4.1 / Num. unique all: 1552 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.1→46.18 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.939 / SU B: 8.76 / SU ML: 0.122 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.2 / ESU R Free: 0.169 / 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: 50.811 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→46.18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.156 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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