+Open data
-Basic information
Entry | Database: PDB / ID: 1wk4 | ||||||
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Title | Crystal structure of ttk003001606 | ||||||
Components | ttk003001606 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / ttk003001606 / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information acyltransferase activity, transferring groups other than amino-acyl groups Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å | ||||||
Authors | Kaminishi, T. / Sakai, H. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of ttk003001606 Authors: Kaminishi, T. / Sakai, H. / Terada, T. / 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 | 1wk4.cif.gz | 111.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wk4.ent.gz | 92.4 KB | Display | PDB format |
PDBx/mmJSON format | 1wk4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wk/1wk4 ftp://data.pdbj.org/pub/pdb/validation_reports/wk/1wk4 | 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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3 |
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Unit cell |
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Details | A monomer is probably the biological unit. |
-Components
#1: Protein | Mass: 19519.062 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SJ05 #2: Chemical | #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: 3 Å3/Da / Density % sol: 58.2 % / Description: The file contains Friedel pairs. |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: MES, sodium formate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.96500, 0.97897, 0.97933 | ||||||||||||
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Detector | Detector: CCD / Date: Apr 11, 2004 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.8→50 Å / Num. obs: 33433 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 16.8 % / Biso Wilson estimate: 73.2 Å2 / Rsym value: 0.097 / Net I/σ(I): 30.7 | ||||||||||||
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 17.2 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 1685 / Rsym value: 0.574 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.8→47.19 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 322005.14 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: the file contains Friedel pairs.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 72.7011 Å2 / ksol: 0.369931 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 73.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→47.19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
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Xplor file |
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