+Open data
-Basic information
Entry | Database: PDB / ID: 1to9 | ||||||
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Title | Crystal structure of THI-4 protein from Bacillus subtilis | ||||||
Components | (THI-4 protein) x 2 | ||||||
Keywords | BIOSYNTHETIC PROTEIN / TenA / Thiamine Biosynthesis / all-alpha / Structural Genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information aminopyrimidine aminohydrolase / thiaminase activity / thiamine diphosphate biosynthetic process / thiamine biosynthetic process / cytosol Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å | ||||||
Authors | Rajan, S.S. / Shuvalova, L. / Yang, X. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of THI-4 protein from Bacillus subtilis Authors: Rajan, S.S. / Shuvalova, L. / Yang, X. / Hussar, C. / Collart, F. / Anderson, W.F. | ||||||
History |
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Remark 999 | SEQUENCE Residue 149 is oxidized in chain B. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1to9.cif.gz | 103.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1to9.ent.gz | 84.7 KB | Display | PDB format |
PDBx/mmJSON format | 1to9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/to/1to9 ftp://data.pdbj.org/pub/pdb/validation_reports/to/1to9 | 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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-Components
#1: Protein | Mass: 30519.750 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: TENA, BSU11650 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P25052 | ||
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#2: Protein | Mass: 30551.750 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: TENA, BSU11650 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P25052 | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.66 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 2M Hexanediol, 0.2M CaCl2, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-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: 2.4→30 Å / Num. all: 21219 / Num. obs: 21219 / % possible obs: 99.7 % / Redundancy: 7 % / Rmerge(I) obs: 0.045 / Rsym value: 0.039 | ||||||||||||||||||
Reflection shell | Resolution: 2.4→2.45 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.117 / Mean I/σ(I) obs: 7.5 / Num. unique all: 1239 / Rsym value: 0.089 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.901 / SU B: 7.675 / SU ML: 0.178 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.446 / ESU R Free: 0.272 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES 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: 41.918 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -2.259 Å / Origin y: -13.3203 Å / Origin z: 16.0012 Å
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Refinement TLS group |
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