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- PDB-1a4x: PYRR, THE BACILLUS SUBTILIS PYRIMIDINE BIOSYNTHETIC OPERON REPRES... -

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Basic information

Entry
Database: PDB / ID: 1a4x
TitlePYRR, THE BACILLUS SUBTILIS PYRIMIDINE BIOSYNTHETIC OPERON REPRESSOR, HEXAMERIC FORM
ComponentsPYRIMIDINE OPERON REGULATORY PROTEIN PYRR
KeywordsTRANSCRIPTION 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
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 / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsTomchick, D.R. / Turner, R.J. / Switzer, R.W. / Smith, J.L.
CitationJournal: 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
DepositionFeb 8, 1998Processing site: BNL
Revision 1.0Aug 5, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 10, 2021Group: Advisory / Derived calculations / Other
Category: pdbx_database_status / pdbx_distant_solvent_atoms ...pdbx_database_status / pdbx_distant_solvent_atoms / pdbx_validate_close_contact / struct_conn / struct_site
Item: _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id ..._pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 2, 2023Group: Database references / Refinement description / Category: 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

Downloads & links

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Assembly

Deposited unit
A: PYRIMIDINE OPERON REGULATORY PROTEIN PYRR
B: PYRIMIDINE OPERON REGULATORY PROTEIN PYRR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7734
Polymers40,5812
Non-polymers1922
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-46 kcal/mol
Surface area15170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.580, 100.580, 275.150
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

NCS oper: (Code: given
Matrix: (-0.556303, 0.830967, -0.004548), (0.830862, 0.556308, 0.013773), (0.013975, 0.003884, -0.999893)
Vector: 0.1598, -0.7474, 137.03529)

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Components

#1: Protein PYRIMIDINE OPERON REGULATORY PROTEIN PYRR / PYRR


Mass: 20290.279 Da / Num. of mol.: 2
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
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 3.4 Å3/Da / Density % sol: 58 %
Crystal growpH: 5.1
Details: PROTEIN WAS CRYSTALLIZED FROM 14-16% PEG 6000, 300 MM AMMONIUM SULFATE, 0.2% BETA-OCTYLGLUCOSIDE, 50 MM SODIUM SUCCINATE, PH 5.1. HEXAGONAL SETTING FOR R 3 2.
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
210 mMTris acetate1droppH7.5
30.2 %beta-octylglucoside1drop
413-16 %PEG60001reservoir
5300 mMammonium sulfate1reservoir
650 mMsodium succinate1reservoirpH5.1

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Sep 1, 1995 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 23877 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 37.8 Å2 / Rsym value: 0.05 / Net I/σ(I): 34
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 3 % / Mean I/σ(I) obs: 8 / Rsym value: 0.158 / % possible all: 97.5
Reflection
*PLUS
Num. measured all: 92317 / Rmerge(I) obs: 0.05

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A3C

1a3c


Resolution: 2.3→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: LYS 40, IN BOTH THE A AND B CHAINS, HAS PHI/PSI VALUES THAT ARE NORMALLY DISALLOWED. IN SOME OTHER PRTASES, THIS PEPTIDE IS TYPICALLY FOUND IN THE CIS CONFORMATION.
RfactorNum. reflection% reflectionSelection details
Rfree0.247 2249 9.7 %RANDOM
Rwork0.211 ---
obs0.211 23799 98.5 %-
Displacement parametersBiso mean: 35.7 Å2
Refinement stepCycle: LAST / Resolution: 2.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2695 0 5 239 2939
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.45
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Rms dev Biso : 30 Å2 / Rms dev position: 1 Å / Weight Biso : 0.5

Ens-IDDom-IDNCS model detailsWeight position
11RESTRAINED100
2250
LS refinement shellResolution: 2.3→2.35 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.294 162 10.5 %
Rwork0.221 1349 -
obs--96.6 %
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.45

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