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- PDB-2igb: Crystal Structure of PyrR, The Regulator Of The Pyrimidine Biosyn... -

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Basic information

Entry
Database: PDB / ID: 2igb
TitleCrystal Structure of PyrR, The Regulator Of The Pyrimidine Biosynthetic Operon In Bacillus caldolyticus, UMP-bound form
ComponentsPyrR bifunctional protein
KeywordsTRANSFERASE / TRANSCRIPTION / TRANSCRIPTION REGULATION / ATTENUATION PROTEIN / RNA-BINDING / PYRIMIDINE BIOSYNTHESIS / PRTASE / URACIL PHOSPHORIBOSYLTRANSFERASE
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
URIDINE-5'-MONOPHOSPHATE / Bifunctional protein PyrR
Similarity search - Component
Biological speciesBacillus caldolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsChander, P. / Switzer, R.L. / Smith, J.L.
CitationJournal: To be Published
Title: PyrR, the regulator of the pyrimidine biosynthetic operon in Bacillus caldolyticus
Authors: Chander, P. / Switzer, R.L. / Smith, J.L.
History
DepositionSep 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,95510
Polymers39,9342
Non-polymers1,0218
Water5,152286
1
A: PyrR bifunctional protein
B: PyrR bifunctional protein
hetero molecules

A: PyrR bifunctional protein
B: PyrR bifunctional protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,91020
Polymers79,8684
Non-polymers2,04216
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Unit cell
Length a, b, c (Å)66.281, 96.752, 63.104
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSGLUGLUAA3 - 653 - 65
21LYSLYSGLUGLUBB3 - 653 - 65
32VALVALVALVALAA95 - 15395 - 153
42VALVALVALVALBB95 - 15395 - 153

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Components

#1: Protein PyrR bifunctional protein / Pyrimidine operon regulatory protein / Uracil phosphoribosyltransferase / UPRTase


Mass: 19967.051 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus caldolyticus (bacteria) / Gene: pyrR / Production host: Escherichia coli (E. coli)
References: UniProt: P41007, uracil phosphoribosyltransferase
#2: Chemical ChemComp-U5P / URIDINE-5'-MONOPHOSPHATE


Mass: 324.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N2O9P
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 2.53 Å3/Da / Density % sol: 51.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M sodium citrate, 0.2M sodium chloride, 1.0M diammonium hydrogen phosphate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97 Å
DetectorDate: Mar 22, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.68→50 Å / Num. obs: 46630 / Redundancy: 7 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.057
Reflection shellResolution: 1.68→1.74 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.93 / Rsym value: 0.62

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1NON

1non


Resolution: 1.68→41.31 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.95 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22375 2356 5.1 %RANDOM
Rwork0.18249 ---
obs0.18452 44224 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.579 Å2
Baniso -1Baniso -2Baniso -3
1-1.45 Å20 Å20 Å2
2---0.57 Å20 Å2
3----0.87 Å2
Refinement stepCycle: LAST / Resolution: 1.68→41.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2843 0 66 286 3195
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222936
X-RAY DIFFRACTIONr_angle_refined_deg1.7021.9973946
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1315341
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.59322.194155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.3815570
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4931550
X-RAY DIFFRACTIONr_chiral_restr0.1390.2455
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022172
X-RAY DIFFRACTIONr_nbd_refined0.2110.21356
X-RAY DIFFRACTIONr_nbtor_refined0.310.21970
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.2261
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2290.291
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3560.241
X-RAY DIFFRACTIONr_mcbond_it1.1981.51778
X-RAY DIFFRACTIONr_mcangle_it1.84622818
X-RAY DIFFRACTIONr_scbond_it2.66131250
X-RAY DIFFRACTIONr_scangle_it4.1874.51128
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 932 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.40.5
medium thermal1.22
LS refinement shellResolution: 1.68→1.73 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 171 -
Rwork0.255 3109 -
obs--95.13 %

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