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- PDB-5iao: Structure and mapping of spontaneous mutational sites of PyrR fro... -

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Basic information

Entry
Database: PDB / ID: 5iao
TitleStructure and mapping of spontaneous mutational sites of PyrR from Mycobacterium tuberculosis
ComponentsBifunctional protein PyrR
KeywordsTRANSFERASE / Uracil phosphoribosyltransferase (UPRTase)
Function / homology
Function and homology information


uracil phosphoribosyltransferase / uracil phosphoribosyltransferase activity / nucleoside metabolic process / peptidoglycan-based cell wall / regulation of DNA-templated transcription
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
5-FLUOROURACIL / Bifunctional protein PyrR / Bifunctional protein PyrR
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.598 Å
AuthorsSivaraman, J. / Ghode, P. / Ramachandran, S.
Funding support Singapore, 1items
OrganizationGrant numberCountry
NUS AcRF tier 1 grantR154000616112 Singapore
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2016
Title: Structure and mapping of spontaneous mutational sites of PyrR from Mycobacterium tuberculosis
Authors: Ghode, P. / Ramachandran, S. / Bifani, P. / Sivaraman, J.
History
DepositionFeb 21, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2016Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bifunctional protein PyrR
B: Bifunctional protein PyrR
C: Bifunctional protein PyrR
D: Bifunctional protein PyrR
E: Bifunctional protein PyrR
F: Bifunctional protein PyrR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,3099
Polymers128,9196
Non-polymers3903
Water6,143341
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8280 Å2
ΔGint7 kcal/mol
Surface area45050 Å2
Unit cell
Length a, b, c (Å)142.836, 127.770, 90.777
Angle α, β, γ (deg.)90.00, 90.38, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Bifunctional protein PyrR


Mass: 21486.447 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25177 / H37Ra) (bacteria)
Strain: ATCC 25177 / H37Ra / Gene: pyrR, MRA_1388 / Production host: Escherichia coli (E. coli)
References: UniProt: A5U281, UniProt: P9WHK3*PLUS, uracil phosphoribosyltransferase
#2: Chemical ChemComp-URF / 5-FLUOROURACIL


Mass: 130.077 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H3FN2O2 / Comment: medication, chemotherapy*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 341 / 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: 3.34 Å3/Da / Density % sol: 63.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M imidazole pH 6.5, 1.0M sodium acetate trihydrate, 10%(v/v) 1,2-Butanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.598→42.24 Å / Num. obs: 188352 / % possible obs: 99.17 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.138 / Net I/σ(I): 7.7
Reflection shellResolution: 2.598→2.691 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1W30

1w30


Resolution: 2.598→42.24 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.89
RfactorNum. reflection% reflection
Rfree0.2376 2006 4.03 %
Rwork0.1951 --
obs0.1969 49742 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.598→42.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7773 0 27 341 8141
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057896
X-RAY DIFFRACTIONf_angle_d0.8610713
X-RAY DIFFRACTIONf_dihedral_angle_d10.4512964
X-RAY DIFFRACTIONf_chiral_restr0.0331278
X-RAY DIFFRACTIONf_plane_restr0.0041413
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5984-2.66340.2721370.25543309X-RAY DIFFRACTION97
2.6634-2.73540.30141370.25063395X-RAY DIFFRACTION99
2.7354-2.81590.32681440.24813371X-RAY DIFFRACTION99
2.8159-2.90670.27041410.24973377X-RAY DIFFRACTION99
2.9067-3.01060.31971450.23223393X-RAY DIFFRACTION99
3.0106-3.13110.31441390.22933397X-RAY DIFFRACTION99
3.1311-3.27350.25941460.22073393X-RAY DIFFRACTION99
3.2735-3.4460.2591410.20693404X-RAY DIFFRACTION99
3.446-3.66180.27361480.19193460X-RAY DIFFRACTION100
3.6618-3.94440.2081440.17183395X-RAY DIFFRACTION100
3.9444-4.3410.20991450.16263440X-RAY DIFFRACTION100
4.341-4.96830.1621410.14453439X-RAY DIFFRACTION100
4.9683-6.25620.21551470.1883482X-RAY DIFFRACTION100
6.2562-42.24880.1821510.17153481X-RAY DIFFRACTION99

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