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Yorodumi- PDB-1non: PyrR, the regulator of the pyrimidine biosynthetic operon in Baci... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1non | ||||||
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Title | PyrR, the regulator of the pyrimidine biosynthetic operon in Bacillus caldolyticus | ||||||
Components | PyrR bifunctional protein | ||||||
Keywords | TRANSCRIPTION / TRANSFERASE / TRANSCRIPTION REGULATION / ATTENUATION PROTEIN / RNA-BINDING PROTEIN / PYRIMIDINE BIOSYNTHESIS / PRTASE / URACIL PHOSPHORIBOSYLTRANSFERASE / BIFUNCTIONAL ENZYME | ||||||
Function / homology | Function and homology information uracil phosphoribosyltransferase / uracil phosphoribosyltransferase activity / DNA-templated transcription termination / RNA binding Similarity search - Function | ||||||
Biological species | Bacillus caldolyticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Switzer, R.L. / Chander, P. / Smith, J.L. / Halbig, K.M. / Miller, J.K. / Bonner, H.K. / Grabner, G.K. | ||||||
Citation | Journal: J.Bacteriol. / Year: 2005 Title: Structure of the Nucleotide Complex of PyrR, the pyr Attenuation Protein from Bacillus caldolyticus, Suggests Dual Regulation by Pyrimidine and Purine Nucleotides Authors: Chander, P. / Halbig, K.M. / Miller, J.K. / Fields, C.J. / Bonner, H.K. / Grabner, G.K. / Switzer, R.L. / Smith, J.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1non.cif.gz | 140.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1non.ent.gz | 112 KB | Display | PDB format |
PDBx/mmJSON format | 1non.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1non_validation.pdf.gz | 453.5 KB | Display | wwPDB validaton report |
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Full document | 1non_full_validation.pdf.gz | 471.1 KB | Display | |
Data in XML | 1non_validation.xml.gz | 29.4 KB | Display | |
Data in CIF | 1non_validation.cif.gz | 41.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/no/1non ftp://data.pdbj.org/pub/pdb/validation_reports/no/1non | HTTPS FTP |
-Related structure data
Related structure data | 1xz8C 1xznC 1a3cS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | biological aassembley is a tetramer; generated from the monomer by the operation X,Y,Z; -X,Y,-Z; 1/2+X,1/2+Y,Z; 1/2-X,1/2+Y,-Z |
-Components
#1: Protein | Mass: 19967.051 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: includes Pyrimidine operon regulatory protein and Uracil phosphoribosyltransferase Source: (gene. exp.) Bacillus caldolyticus (bacteria) / Gene: pyrr / Plasmid: pSHCO2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 References: UniProt: P41007, uracil phosphoribosyltransferase #2: 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: 2.28 Å3/Da / Density % sol: 45.6 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: PEG 400, ammonium chloride, magnesium chloride, cacodylate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 30, 2002 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 26925 / Num. obs: 25768 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 52.3 Å2 / Rmerge(I) obs: 0.035 / Rsym value: 0.211 / Net I/σ(I): 19.1 |
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 1 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 19.1 / Num. unique all: 2376 / Rsym value: 0.211 / % possible all: 92 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1A3C Resolution: 2.4→50 Å / Cross valid method: THROUGHOUT / σ(F): 2.4 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.4→50 Å
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Refine LS restraints |
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