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- PDB-5hkf: Crystal structure of Mycobacterium tuberculosis H37Rv orotate pho... -

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Basic information

Entry
Database: PDB / ID: 5hkf
TitleCrystal structure of Mycobacterium tuberculosis H37Rv orotate phosphoribosyltransferase in complex with 5-phospho-alpha-D-ribosyl 1-diphosphate (PRPP)
ComponentsOrotate phosphoribosyltransferase
KeywordsTRANSFERASE / OPRT / de novo pyrimidine nucleotide synthesis / PRPP complex
Function / homology
Function and homology information


UMP biosynthetic process / orotate phosphoribosyltransferase / orotate phosphoribosyltransferase activity / pyrimidine nucleobase biosynthetic process / orotidine-5'-phosphate decarboxylase activity / 'de novo' UMP biosynthetic process / magnesium ion binding
Similarity search - Function
Orotate phosphoribosyl transferase domain / Orotate phosphoribosyltransferase / Rossmann fold - #2020 / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-PRP / Orotate phosphoribosyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsDonini, S. / Ferraris, D.M. / Bolognesi, G. / Rizzi, M.
Funding support Italy, 1items
OrganizationGrant numberCountry
FP7-HEALTH260872 Italy
CitationJournal: Sci Rep / Year: 2017
Title: Structural investigations on orotate phosphoribosyltransferase from Mycobacterium tuberculosis, a key enzyme of the de novo pyrimidine biosynthesis.
Authors: Donini, S. / Ferraris, D.M. / Miggiano, R. / Massarotti, A. / Rizzi, M.
History
DepositionJan 14, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Orotate phosphoribosyltransferase
B: Orotate phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1864
Polymers40,4062
Non-polymers7802
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-26 kcal/mol
Surface area13620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.201, 58.629, 57.224
Angle α, β, γ (deg.)90.00, 116.86, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Orotate phosphoribosyltransferase / OPRTase


Mass: 20202.830 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The overall electron density presents two gaps between the residues 1-3 and 95-105, numbered from the N-terminal methionine. No His-tag was traced in this case.
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Gene: pyrE, umpA, Rv0382c, MTV036.17c / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P9WHK9, orotate phosphoribosyltransferase
#2: Sugar ChemComp-PRP / 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose / ALPHA-PHOSPHORIBOSYLPYROPHOSPHORIC ACID / 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribose / 1-O-pyrophosphono-5-O-phosphono-D-ribose / 1-O-pyrophosphono-5-O-phosphono-ribose


Type: D-saccharide / Mass: 390.070 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H13O14P3
IdentifierTypeProgram
a-D-Ribf1PO35PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.23 Å3/Da / Density % sol: 44.78 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 0.1M HEPES pH 7.5, 10% (w/v) PEG6000, 5% (v/v) MPD, 1mM PRPP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.899 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.899 Å / Relative weight: 1
ReflectionResolution: 2.25→51.05 Å / Num. obs: 15782 / % possible obs: 99.3 % / Redundancy: 4.7 % / Biso Wilson estimate: 27.62 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 19.66
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.131 / Mean I/σ(I) obs: 7.08 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
SCALAdata scaling
ARPmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HKI

5hki


Resolution: 2.25→51.05 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.93 / SU B: 8.183 / SU ML: 0.199 / Cross valid method: THROUGHOUT / ESU R: 0.319 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2334 788 5 %RANDOM
Rwork0.18686 ---
obs0.18942 14982 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.418 Å2
Baniso -1Baniso -2Baniso -3
1-4.8 Å20 Å22.31 Å2
2---1.92 Å20 Å2
3----3.45 Å2
Refinement stepCycle: LAST / Resolution: 2.25→51.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2449 0 44 87 2580
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192521
X-RAY DIFFRACTIONr_bond_other_d0.0010.022459
X-RAY DIFFRACTIONr_angle_refined_deg1.6911.9793428
X-RAY DIFFRACTIONr_angle_other_deg0.81835595
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8145321
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.11321.524105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.46715396
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7451532
X-RAY DIFFRACTIONr_chiral_restr0.0780.2417
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022792
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02560
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8423.8651305
X-RAY DIFFRACTIONr_mcbond_other2.8433.8641304
X-RAY DIFFRACTIONr_mcangle_it4.255.7611619
X-RAY DIFFRACTIONr_mcangle_other4.2495.7631620
X-RAY DIFFRACTIONr_scbond_it3.4764.4521216
X-RAY DIFFRACTIONr_scbond_other3.4574.4541212
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3326.5251804
X-RAY DIFFRACTIONr_long_range_B_refined7.21631.3022787
X-RAY DIFFRACTIONr_long_range_B_other7.21831.292768
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 57 -
Rwork0.235 1098 -
obs--99.57 %

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