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Yorodumi- PDB-1z72: Structure of a putative transcriptional regulator from Streptococ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1z72 | ||||||
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Title | Structure of a putative transcriptional regulator from Streptococcus pneumoniae | ||||||
Components | transcriptional regulator, putativeTranscriptional regulation | ||||||
Keywords | Transcription Regulator / Streptococcus pneumoniae / transcriptional regulator / 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 / metal ion binding Similarity search - Function | ||||||
Biological species | Streptococcus pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.45 Å | ||||||
Authors | Cuff, M.E. / Zhou, M. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Structure of a putative transcriptional regulator from Streptococcus pneumoniae Authors: Cuff, M.E. / Zhou, M. / Joachimiak, A. | ||||||
History |
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Remark 300 | BIOMOLECULE According to author, the biological unit has not been experimentally identified, but ...BIOMOLECULE According to author, the biological unit has not been experimentally identified, but the two molecules in the asymmetric unit share both hydrophobic and hydrophilic contacts. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1z72.cif.gz | 119.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1z72.ent.gz | 98.6 KB | Display | PDB format |
PDBx/mmJSON format | 1z72.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z7/1z72 ftp://data.pdbj.org/pub/pdb/validation_reports/z7/1z72 | 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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Unit cell |
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Details | unknown, possible dimer |
-Components
#1: Protein | Mass: 26101.895 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: TIGR4 / Gene: SP0716 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q97RS7, UniProt: A0A0H2UP67*PLUS #2: Chemical | #3: Chemical | ChemComp-MG / | #4: 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: 3.2 Å3/Da / Density % sol: 61.4 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Tacsimate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 105 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97908, 0.97919 | |||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 7, 2005 | |||||||||
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.45→50 Å / Num. all: 116194 / Num. obs: 116194 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 | |||||||||
Reflection shell | Resolution: 1.45→1.51 Å / Redundancy: 3 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.4 / % possible all: 91.5 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.45→43.1 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.429 / SU ML: 0.028 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.051 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The loop region between residues 193 and 198 of molecule A and B is disordered. Whereas the location of ARG 195 is clear in electron ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The loop region between residues 193 and 198 of molecule A and B is disordered. Whereas the location of ARG 195 is clear in electron density maps, the positions of residues 194, 196, and 197 are not.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.868 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→43.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.488 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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