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Yorodumi- PDB-1v8d: Crystal structure of the conserved hypothetical protein TT1679 fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1v8d | ||||||
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Title | Crystal structure of the conserved hypothetical protein TT1679 from Thermus thermophilus | ||||||
Components | hypothetical protein (TT1679) | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / X-ray craytallography / hypothetical protein / Thermus thermophilus / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Hypothetical protein TT1679 / Protein of unknown function DUF436 / Protein of unknown function (DUF436) / Aminoglycoside 3-N-acetyltransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / UPF0340 protein TT_C0214 Function and homology information | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.16 Å | ||||||
Authors | Kishishita, S. / Terada, T. / Shirouzu, M. / Kuramitsu, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of the conserved hypothetical protein TT1679 from Thermus thermophilus HB8 Authors: Kishishita, S. / Terada, T. / Shirouzu, M. / Kuramitsu, S. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1v8d.cif.gz | 126.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1v8d.ent.gz | 97.8 KB | Display | PDB format |
PDBx/mmJSON format | 1v8d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1v8d_validation.pdf.gz | 391 KB | Display | wwPDB validaton report |
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Full document | 1v8d_full_validation.pdf.gz | 411.1 KB | Display | |
Data in XML | 1v8d_validation.xml.gz | 14.8 KB | Display | |
Data in CIF | 1v8d_validation.cif.gz | 24.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v8/1v8d ftp://data.pdbj.org/pub/pdb/validation_reports/v8/1v8d | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 25184.412 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pET11b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q72L49 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.72 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG3350, MPD, Sodium Thiocyanate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.15→50 Å / Num. all: 33860 / Num. obs: 32472 / % possible obs: 93.1 % / Observed criterion σ(I): 81769 / Redundancy: 2.4 % / Biso Wilson estimate: 12.3 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 17.3 | ||||||||||||||||||
Reflection shell | Resolution: 2.15→2.23 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.095 / Num. unique all: 2619 / % possible all: 73 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.16→34.55 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 497221.82 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Maximum likelihood
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 58.777 Å2 / ksol: 0.346131 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.16→34.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.28 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Xplor file |
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