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Yorodumi- PDB-4oqp: Structure of the effector-binding domain of deoxyribonucleoside r... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4oqp | ||||||
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Title | Structure of the effector-binding domain of deoxyribonucleoside regulator DeoR from Bacillus subtilis in complex with deoxyribose-5-phosphate | ||||||
Components | Deoxyribonucleoside regulator | ||||||
Keywords | TRANSCRIPTION / Rossmann Fold / Sugar-binding transcriptional regulator / Schiff base | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacillus subtilis subsp. subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Rezacova, P. / Skerlova, J. | ||||||
Citation | Journal: Febs J. / Year: 2014 Title: Structure of the effector-binding domain of deoxyribonucleoside regulator DeoR from Bacillus subtilis. Authors: Skerlova, J. / Fabry, M. / Hubalek, M. / Otwinowski, Z. / Rezacova, P. #1: Journal: Mol.Microbiol. / Year: 2008 Title: Crystal structures of the effector-binding domain of repressor Central glycolytic gene Regulator from Bacillus subtilis reveal ligand-induced structural changes upon binding of several glycolytic intermediates. Authors: Rezacova, P. / Kozisek, M. / Moy, S.F. / Sieglova, I. / Joachimiak, A. / Machius, M. / Otwinowski, Z. #2: Journal: Cryst.GrowthDes. / Year: 2013 Title: Crystallization of the Effector-Binding Domain of Repressor DeoR from Bacillus subtilis Authors: Pisackova, J. / Prochazkova, K. / Fabry, M. / Rezacova, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4oqp.cif.gz | 128.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4oqp.ent.gz | 99.1 KB | Display | PDB format |
PDBx/mmJSON format | 4oqp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4oqp_validation.pdf.gz | 431.7 KB | Display | wwPDB validaton report |
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Full document | 4oqp_full_validation.pdf.gz | 431.7 KB | Display | |
Data in XML | 4oqp_validation.xml.gz | 14.4 KB | Display | |
Data in CIF | 4oqp_validation.cif.gz | 21.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oq/4oqp ftp://data.pdbj.org/pub/pdb/validation_reports/oq/4oqp | HTTPS FTP |
-Related structure data
Related structure data | 4oqqC 3nzeS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 29371.447 Da / Num. of mol.: 1 / Fragment: C-terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria) Strain: 168 / Gene: deoR, yxxC, BSU39430 / Plasmid: pET151 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P39140 |
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-Non-polymers , 6 types, 271 molecules
#2: Chemical | ChemComp-PED / | ||||||
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#3: Chemical | ChemComp-CD / | ||||||
#4: Chemical | #5: Chemical | ChemComp-CO / | #6: Chemical | ChemComp-MG / | #7: Water | ChemComp-HOH / | |
-Details
Nonpolymer details | THE ORGINAL SUGAR D 2-DEOXYRIBOSE-5-PHOSPHATE WAS COVALENTLY BOUND TO LYS141 BY SCHIFF BASE. THE ...THE ORGINAL SUGAR D 2-DEOXYRIBOS |
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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: 2.36 Å3/Da / Density % sol: 47.97 % |
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Crystal grow | Temperature: 291 K / pH: 7.5 Details: 0.08 M HEPES, 9.6% (w/v) PEG 3350, 4 mM CoCl2, 4 mM CdCl2, 4 mM MgCl2, and 4 mM NiCl2; 16.5 mg/mL protein in 20 mM trisodium citrate pH 7.0, 150 mM NaCl, 0.02% (v/v) 2-mercaptoethanol, 50 mM ...Details: 0.08 M HEPES, 9.6% (w/v) PEG 3350, 4 mM CoCl2, 4 mM CdCl2, 4 mM MgCl2, and 4 mM NiCl2; 16.5 mg/mL protein in 20 mM trisodium citrate pH 7.0, 150 mM NaCl, 0.02% (v/v) 2-mercaptoethanol, 50 mM deoxyribose-5-phosphate; protein:reservoir 2:1, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 17, 2012 Details: DOUBLE CRYSTAL MONOCHROMATOR WITH 2 SETS OF RH-SOATED SILLICON AND GLASS MIRRORS |
Radiation | Monochromator: SI(111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 34660 / % possible obs: 93.5 % / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rmerge(I) obs: 0.04 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.255 / Mean I/σ(I) obs: 2.8 / % possible all: 62.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3NZE Resolution: 1.6→19.77 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.784 / SU ML: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.082 / ESU R Free: 0.085 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.6 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→19.77 Å
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Refine LS restraints |
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