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Yorodumi- PDB-1a3c: PYRR, THE BACILLUS SUBTILIS PYRIMIDINE BIOSYNTHETIC OPERON REPRES... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1a3c | ||||||
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Title | PYRR, THE BACILLUS SUBTILIS PYRIMIDINE BIOSYNTHETIC OPERON REPRESSOR, DIMERIC FORM | ||||||
Components | PYRIMIDINE OPERON REGULATORY PROTEIN PYRR | ||||||
Keywords | TRANSCRIPTION REGULATION / ATTENUATION PROTEIN / RNA-BINDING PROTEIN / PYRIMIDINE BIOSYNTHESIS / TRANSFERASE / PRTASE / 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 subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å | ||||||
Authors | Tomchick, D.R. / Turner, R.J. / Switzer, R.W. / Smith, J.L. | ||||||
Citation | Journal: Structure / Year: 1998 Title: Adaptation of an enzyme to regulatory function: structure of Bacillus subtilis PyrR, a pyr RNA-binding attenuation protein and uracil phosphoribosyltransferase. Authors: Tomchick, D.R. / Turner, R.J. / 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 | 1a3c.cif.gz | 54.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a3c.ent.gz | 39.3 KB | Display | PDB format |
PDBx/mmJSON format | 1a3c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1a3c_validation.pdf.gz | 444.9 KB | Display | wwPDB validaton report |
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Full document | 1a3c_full_validation.pdf.gz | 450.2 KB | Display | |
Data in XML | 1a3c_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | 1a3c_validation.cif.gz | 18.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a3/1a3c ftp://data.pdbj.org/pub/pdb/validation_reports/a3/1a3c | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 20290.279 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: PYRR / Plasmid: PTSROX3 / Production host: Escherichia coli (E. coli) / Strain (production host): S0408 / References: UniProt: P39765 | ||||
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#2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: 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: 2.4 Å3/Da / Density % sol: 40 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.1 Details: PROTEIN WAS CRYSTALLIZED FROM 13-16% PEG 6000, 300 MM AMMONIUM SULFATE, 0.2% BETA-OCTYLGLUCOSIDE, 50 MM SODIUM SUCCINATE, PH 5.1, AND 1 MM SAMARIUM NITRATE. | ||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop / pH: 7.5 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9799 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 1995 / Details: MIRRORS |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9799 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→40 Å / Num. obs: 26609 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 14.6 Å2 / Rsym value: 0.085 / Net I/σ(I): 11.7 |
Reflection | *PLUS Num. measured all: 104445 / Rmerge(I) obs: 0.085 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.6→15 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: THE POSITIONAL COORDINATES OF SM 182, THE SAMARIUM ION ON THE CRYSTALLOGRAPHIC TWO-FOLD AXIS, WAS HELD AT 0,0,0 DURING THE REFINEMENT TO PREVENT OSCILLATION OF THE PROTEIN POSITIONAL ...Details: THE POSITIONAL COORDINATES OF SM 182, THE SAMARIUM ION ON THE CRYSTALLOGRAPHIC TWO-FOLD AXIS, WAS HELD AT 0,0,0 DURING THE REFINEMENT TO PREVENT OSCILLATION OF THE PROTEIN POSITIONAL COORDINATES. THE MODEL INCLUDES AN X-PLOR BULK SOLVENT CORRECTION WITH PARAMETERS SOLRAD=0.25, DENSITY=0.55, B=100. LYS 40 HAS PHI/PSI VALUES THAT ARE NORMALLY DISALLOWED. IN SOME OTHER PRTASES, THIS PEPTIDE IS TYPICALLY FOUND IN THE CIS CONFORMATION. SEVENTEEN RESIDUES ARE MODELED IN ALTERNATIVE CONFORMATIONS. THESE ARE LEU 8, GLU 10, GLN 11, ARG 14, ARG 19, GLU 52, GLN 56, THR 70, LYS 100, VAL 107, VAL 122, ARG 126, SER 128, VAL 136, ILE 145, LYS 152, AND MET 163. ONLY THE MAIN CHAIN AND C-BETA ATOMS OF ASN 180 WERE VISIBLE IN THE ELECTRON DENSITY. LYS 40 HAS PHI/PSI VALUES THAT ARE NORMALLY DISALLOWED. IN SOME OTHER PRTASES, THIS PEPTIDE IS TYPICALLY FOUND IN THE CIS CONFORMATION.
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Displacement parameters | Biso mean: 17 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.63 Å / Total num. of bins used: 20
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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