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Yorodumi- PDB-2d4p: Crystal structure of TTHA1254 (wild type) from Thermus thermophil... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2d4p | ||||||
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Title | Crystal structure of TTHA1254 (wild type) from Thermus thermophilus HB8 | ||||||
Components | hypothetical protein TTHA1254Hypothesis | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information N-acetyltransferase activity / acyltransferase activity, transferring groups other than amino-acyl groups Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Mizohata, E. / Uchikubo, T. / Kinoshita, Y. / Terada, T. / Shirouzu, M. / Kuramitsu, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of TTHA1254 (wild type) from Thermus thermophilus HB8 Authors: Mizohata, E. / Uchikubo, T. / Kinoshita, Y. / 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 | 2d4p.cif.gz | 41.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2d4p.ent.gz | 28.2 KB | Display | PDB format |
PDBx/mmJSON format | 2d4p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d4/2d4p ftp://data.pdbj.org/pub/pdb/validation_reports/d4/2d4p | HTTPS FTP |
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-Related structure data
Related structure data | 2d4oS S: Starting model for refinement |
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Similar structure data | |
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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-Components
#1: Protein | Mass: 15484.720 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q72J89, UniProt: Q5SIW0*PLUS |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.62 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: PEG3350, Tris, NaCl, Ammonium nitrate, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 10, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 18129 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2D4O Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.945 / SU ML: 0.062 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.089 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.655 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20 /
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Refinement TLS params. | Method: refined / Origin x: 16.2813 Å / Origin y: 21.8618 Å / Origin z: 25.2623 Å
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