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- PDB-4p82: Structure of PyrR protein from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 4p82
TitleStructure of PyrR protein from Bacillus subtilis
ComponentsBifunctional protein PyrR
KeywordsUNKNOWN FUNCTION / RNA binding proteins / reconstructed amino acid sequence
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 subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsPerica, T. / Kondo, Y. / Tiwari, S. / McLaughlin, S. / Steward, A. / Reuter, N. / Clarke, J. / Teichmann, S.A.
CitationJournal: Science / Year: 2014
Title: Evolution of oligomeric state through allosteric pathways that mimic ligand binding.
Authors: Perica, T. / Kondo, Y. / Tiwari, S.P. / McLaughlin, S.H. / Kemplen, K.R. / Zhang, X. / Steward, A. / Reuter, N. / Clarke, J. / Teichmann, S.A.
History
DepositionMar 30, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 31, 2014Group: Database references
Revision 1.2Dec 20, 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: Bifunctional protein PyrR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5282
Polymers20,4321
Non-polymers961
Water2,756153
1
A: Bifunctional protein PyrR
hetero molecules

A: Bifunctional protein PyrR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0574
Polymers40,8652
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area2230 Å2
ΔGint-46 kcal/mol
Surface area17000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.540, 57.600, 54.770
Angle α, β, γ (deg.)90.00, 128.39, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-304-

HOH

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Components

#1: Protein Bifunctional protein PyrR


Mass: 20432.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: pyrR, BSU15470 / Plasmid: pRSET / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41
References: UniProt: P39765, uracil phosphoribosyltransferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 46.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 2.5 M NaCl, 0.1M Acetate pH 4.5, 0.2M Li2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.3→42.93 Å / Num. obs: 42730 / % possible obs: 98.2 % / Redundancy: 3.4 % / Net I/σ(I): 9.5
Reflection shellResolution: 1.3→1.33 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.453 / Mean I/σ(I) obs: 2.3 / % possible all: 96.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1a3c

1a3c


Resolution: 1.3→42.93 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / SU B: 0.898 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20571 2272 5 %RANDOM
Rwork0.17882 ---
obs0.18014 42730 98.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.313 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å2-0 Å2
2--0.18 Å20 Å2
3----0.02 Å2
Refinement stepCycle: 1 / Resolution: 1.3→42.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1404 0 5 153 1562
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0191518
X-RAY DIFFRACTIONr_bond_other_d0.0020.021519
X-RAY DIFFRACTIONr_angle_refined_deg2.3981.9882068
X-RAY DIFFRACTIONr_angle_other_deg0.98333499
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1795201
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.1724.65873
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.35415295
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9571516
X-RAY DIFFRACTIONr_chiral_restr0.1330.2244
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021758
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02318
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5521.628765
X-RAY DIFFRACTIONr_mcbond_other2.5331.625764
X-RAY DIFFRACTIONr_mcangle_it3.9342.438970
X-RAY DIFFRACTIONr_mcangle_other3.9322.441971
X-RAY DIFFRACTIONr_scbond_it3.7032.003751
X-RAY DIFFRACTIONr_scbond_other3.7072.011748
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5922.8511088
X-RAY DIFFRACTIONr_long_range_B_refined8.05414.1081740
X-RAY DIFFRACTIONr_long_range_B_other7.86513.5841689
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 160 -
Rwork0.263 3089 -
obs--95.81 %

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