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Yorodumi- PDB-1j3m: Crystal structure of the conserved hypothetical protein TT1751 fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1j3m | ||||||
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Title | Crystal structure of the conserved hypothetical protein TT1751 from Thermus thermophilus HB8 | ||||||
Components | the conserved hypothetical protein TT1751 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / hypothetical / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information TT1751-like domain / Uncharacterised conserved protein UCP021774 / Domain of unknown function DUF302 / TT1751-like domain superfamily / Domain of unknown function DUF302 / TATA-Binding Protein / 2-Layer Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å | ||||||
Authors | Kishishita, S. / Terada, T. / Shirouzu, M. / Kuramitsu, S. / Park, S.-Y. / Tame, R.H. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: Proteins / Year: 2004 Title: Crystal structure of a conserved hypothetical protein TT1751 from Thermus thermophilus HB8 Authors: Kishishita, S. / Tatsuguchi, A. / Ushikoshi-Nakayama, R. / Terada, T. / Kuramitsu, S. / Park, S.-Y. / Tame, J.R. / Shirouzu, M. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1j3m.cif.gz | 61.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1j3m.ent.gz | 45.3 KB | Display | PDB format |
PDBx/mmJSON format | 1j3m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1j3m_validation.pdf.gz | 388.8 KB | Display | wwPDB validaton report |
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Full document | 1j3m_full_validation.pdf.gz | 395.4 KB | Display | |
Data in XML | 1j3m_validation.xml.gz | 6.9 KB | Display | |
Data in CIF | 1j3m_validation.cif.gz | 10.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j3/1j3m ftp://data.pdbj.org/pub/pdb/validation_reports/j3/1j3m | HTTPS FTP |
-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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Unit cell |
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-Components
#1: Protein | Mass: 13973.396 Da / Num. of mol.: 2 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: Q84BQ8 #2: Chemical | ChemComp-SO3 / | #3: 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: 2.34 Å3/Da / Density % sol: 47.51 % |
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Crystal grow | Temperature: 293 K / Method: microbatch crystallization / pH: 5.6 Details: PEGMME 5000, Ammonium Sulfate, pH 5.6, Microbatch Crystallization, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.9804, 0.9808, 0.9825, 0.9720 | |||||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 4, 2002 / Details: monochromator | |||||||||||||||
Radiation | Monochromator: Si 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2→50 Å / Num. obs: 16980 / % possible obs: 97.9 % / Observed criterion σ(I): 70405 / Redundancy: 4.1 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 16.8 | |||||||||||||||
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.138 / % possible all: 83.8 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.912 / SU B: 5.188 / SU ML: 0.146 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.204 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.423 Å2
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.006→2.058 Å / Total num. of bins used: 20 /
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