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- PDB-1a3c: PYRR, THE BACILLUS SUBTILIS PYRIMIDINE BIOSYNTHETIC OPERON REPRES... -

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Basic information

Entry
Database: PDB / ID: 1a3c
TitlePYRR, THE BACILLUS SUBTILIS PYRIMIDINE BIOSYNTHETIC OPERON REPRESSOR, DIMERIC 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
SAMARIUM (III) ION / Bifunctional protein PyrR
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 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
DepositionJan 20, 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 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Mar 21, 2018Group: Advisory / Derived calculations / Other
Category: pdbx_database_status / pdbx_distant_solvent_atoms ...pdbx_database_status / pdbx_distant_solvent_atoms / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _pdbx_database_status.process_site
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PYRIMIDINE OPERON REGULATORY PROTEIN PYRR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6874
Polymers20,2901
Non-polymers3973
Water4,630257
1
A: PYRIMIDINE OPERON REGULATORY PROTEIN PYRR
hetero molecules

A: PYRIMIDINE OPERON REGULATORY PROTEIN PYRR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3748
Polymers40,5812
Non-polymers7946
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)76.700, 57.700, 55.000
Angle α, β, γ (deg.)90.00, 129.00, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-182-

SM

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Components

#1: Protein PYRIMIDINE OPERON REGULATORY PROTEIN PYRR / PYRR


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
#2: Chemical ChemComp-SM / SAMARIUM (III) ION / Samarium


Mass: 150.360 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Sm
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 257 / 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: 2.4 Å3/Da / Density % sol: 40 %
Crystal growpH: 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
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: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9799
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 1995 / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9799 Å / Relative weight: 1
ReflectionResolution: 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

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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: 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.
RfactorNum. reflection% reflectionSelection details
Rfree0.233 2376 10 %RANDOM
Rwork0.192 ---
obs0.192 24217 98 %-
Displacement parametersBiso mean: 17 Å2
Refinement stepCycle: LAST / Resolution: 1.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1379 0 7 263 1649
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_deg1.6
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_d1.58
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
LS refinement shellResolution: 1.6→1.63 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 117 9.6 %
Rwork0.225 1054 -
obs--98 %
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_deg1.58

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