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- PDB-1non: PyrR, the regulator of the pyrimidine biosynthetic operon in Baci... -

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Basic information

Entry
Database: PDB / ID: 1non
TitlePyrR, the regulator of the pyrimidine biosynthetic operon in Bacillus caldolyticus
ComponentsPyrR bifunctional protein
KeywordsTRANSCRIPTION / 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
Bifunctional protein PyrR / : / Rossmann fold - #2020 / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Bifunctional protein PyrR
Similarity search - Component
Biological speciesBacillus caldolyticus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSwitzer, R.L. / Chander, P. / Smith, J.L. / Halbig, K.M. / Miller, J.K. / Bonner, H.K. / Grabner, G.K.
CitationJournal: 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
DepositionJan 16, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PyrR bifunctional protein
B: PyrR bifunctional protein
C: PyrR bifunctional protein
D: PyrR bifunctional protein


Theoretical massNumber of molelcules
Total (without water)79,8684
Polymers79,8684
Non-polymers00
Water6,449358
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)193.600, 60.740, 59.207
Angle α, β, γ (deg.)90.00, 97.81, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121
Detailsbiological 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

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Components

#1: Protein
PyrR bifunctional protein / E.C.2.4.2.9


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 / water


Mass: 18.015 Da / Num. of mol.: 358 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 45.6 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 30, 2002
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A3C

1a3c


Resolution: 2.4→50 Å / Cross valid method: THROUGHOUT / σ(F): 2.4 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1283 5 %random
Rwork0.192 ---
all-26925 --
obs-25768 --
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5040 0 0 358 5398
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_bond_d0.005

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