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- PDB-5e38: Structural basis of mapping the spontaneous mutations with 5-flou... -

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Basic information

Entry
Database: PDB / ID: 5.0E+38
TitleStructural basis of mapping the spontaneous mutations with 5-flourouracil in uracil phosphoribosyltransferase from Mycobacterium tuberculosis
ComponentsUracil phosphoribosyltransferase
KeywordsTRANSFERASE / uracil phosphoribosyltransferase / Mycobacterium tuberculosis / mutants
Function / homology
Function and homology information


uracil salvage / uracil phosphoribosyltransferase / uracil phosphoribosyltransferase activity / UMP salvage / nucleoside metabolic process / GTP binding / magnesium ion binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Uracil phosphoribosyltransferase, bacterial-type / Uracil phosphoribosyl transferase / Uracil phosphoribosyltransferase / Rossmann fold - #2020 / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Uracil phosphoribosyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsGhode, P. / Jobichen, C. / Ramachandran, S. / Bifani, P. / Sivaraman, J.
Funding support Singapore, 1items
OrganizationGrant numberCountry
National University of SingaporeAcademic Research Grant Singapore
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2015
Title: Structural basis of mapping the spontaneous mutations with 5-flurouracil in uracil phosphoribosyltransferase from Mycobacterium tuberculosis
Authors: Ghode, P. / Jobichen, C. / Ramachandran, S. / Bifani, P. / Sivaraman, J.
History
DepositionOct 2, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Database references
Revision 1.2Nov 11, 2015Group: Database references
Revision 1.3Nov 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 / struct_ncs_dom_lim
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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uracil phosphoribosyltransferase
B: Uracil phosphoribosyltransferase
C: Uracil phosphoribosyltransferase
D: Uracil phosphoribosyltransferase


Theoretical massNumber of molelcules
Total (without water)90,6444
Polymers90,6444
Non-polymers00
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10470 Å2
ΔGint-69 kcal/mol
Surface area31020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.089, 118.089, 77.812
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 2:32 or resseq 34:44 or resseq...
21(chain C and (resseq 2:32 or resseq 34:44 or resseq...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNLEULEU(chain A and (resseq 2:32 or resseq 34:44 or resseq...AA2 - 3211 - 41
12GLUGLUTHRTHR(chain A and (resseq 2:32 or resseq 34:44 or resseq...AA34 - 4443 - 53
13ASPASPALAALA(chain A and (resseq 2:32 or resseq 34:44 or resseq...AA46 - 4755 - 56
14GLUGLULEULEU(chain A and (resseq 2:32 or resseq 34:44 or resseq...AA50 - 7659 - 85
15ALAALAPROPRO(chain A and (resseq 2:32 or resseq 34:44 or resseq...AA78 - 9187 - 100
16GLUGLUGLUGLU(chain A and (resseq 2:32 or resseq 34:44 or resseq...AA92101
17GLYGLYPHEPHE(chain A and (resseq 2:32 or resseq 34:44 or resseq...AA-6 - 2043 - 213
18GLYGLYPHEPHE(chain A and (resseq 2:32 or resseq 34:44 or resseq...AA-6 - 2043 - 213
19GLYGLYPHEPHE(chain A and (resseq 2:32 or resseq 34:44 or resseq...AA-6 - 2043 - 213
110GLYGLYPHEPHE(chain A and (resseq 2:32 or resseq 34:44 or resseq...AA-6 - 2043 - 213
21GLNGLNLEULEU(chain C and (resseq 2:32 or resseq 34:44 or resseq...CC2 - 3211 - 41
22GLUGLUTHRTHR(chain C and (resseq 2:32 or resseq 34:44 or resseq...CC34 - 4443 - 53
23ASPASPALAALA(chain C and (resseq 2:32 or resseq 34:44 or resseq...CC46 - 4755 - 56
24GLUGLUVALVAL(chain C and (resseq 2:32 or resseq 34:44 or resseq...CC50 - 5259 - 61
25PROPROPROPRO(chain C and (resseq 2:32 or resseq 34:44 or resseq...CC5362
26ALAALAPHEPHE(chain C and (resseq 2:32 or resseq 34:44 or resseq...CC0 - 2049 - 213
27ALAALAPHEPHE(chain C and (resseq 2:32 or resseq 34:44 or resseq...CC0 - 2049 - 213
28ALAALAPHEPHE(chain C and (resseq 2:32 or resseq 34:44 or resseq...CC0 - 2049 - 213
29ALAALAPHEPHE(chain C and (resseq 2:32 or resseq 34:44 or resseq...CC0 - 2049 - 213

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Components

#1: Protein
Uracil phosphoribosyltransferase / UMP pyrophosphorylase / UPRTase


Mass: 22660.967 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: upp, Rv3309c, MTV016.08c / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner
References: UniProt: P9WFF3, uracil phosphoribosyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 3.28 Å3/Da / Density % sol: 62.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: Sodium formate

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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 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.438
ReflectionResolution: 3→33 Å / Num. obs: 22764 / % possible obs: 97.1 % / Redundancy: 6 % / Rsym value: 0.19 / Net I/σ(I): 7.8
Reflection shellResolution: 3→3.05 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 3.95 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1O5O

1o5o


Resolution: 3→31.224 Å / Cross valid method: FREE R-VALUE / σ(F): 0.09 / Phase error: 24.64 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2647 2068 8.83 %
Rwork0.2047 --
obs0.2112 22764 96.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→31.224 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5681 0 0 28 5709
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015773
X-RAY DIFFRACTIONf_angle_d1.3877890
X-RAY DIFFRACTIONf_dihedral_angle_d15.2323457
X-RAY DIFFRACTIONf_chiral_restr0.063966
X-RAY DIFFRACTIONf_plane_restr0.0091050
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1436X-RAY DIFFRACTION15.468TORSIONAL
12C1436X-RAY DIFFRACTION15.468TORSIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0014-3.07640.30851520.22251556X-RAY DIFFRACTION90
3.0764-3.15940.32381460.21741568X-RAY DIFFRACTION91
3.1594-3.25220.29011510.22841579X-RAY DIFFRACTION90
3.2522-3.3570.29661390.2141567X-RAY DIFFRACTION90
3.357-3.47680.2471370.20761520X-RAY DIFFRACTION89
3.4768-3.61570.31361360.22461406X-RAY DIFFRACTION81
3.6157-3.77990.31511240.21821373X-RAY DIFFRACTION80
3.7799-3.97860.30741450.23561529X-RAY DIFFRACTION88
3.9786-4.2270.25311510.19221482X-RAY DIFFRACTION85
4.227-4.5520.23361490.17571595X-RAY DIFFRACTION91
4.552-5.00760.23431420.17031529X-RAY DIFFRACTION90
5.0076-5.72650.21151480.19331579X-RAY DIFFRACTION91
5.7265-7.19320.22811350.21451565X-RAY DIFFRACTION91
7.1932-27.42220.22131510.20191516X-RAY DIFFRACTION87

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