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

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Basic information

Entry
Database: PDB / ID: 5hkl
TitleCrystal structure of Mycobacterium tuberculosis H37Rv orotate phosphoribosyltransferase in complex with inorganic phosphate
ComponentsOrotate phosphoribosyltransferase
KeywordsTRANSFERASE / OPRT / de novo pyrimidine nucleotide synthesis / inorganic phosphate complex
Function / homology
Function and homology information


UMP biosynthetic process / orotate phosphoribosyltransferase / orotate phosphoribosyltransferase activity / pyrimidine nucleobase biosynthetic process / '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
PHOSPHATE ION / Orotate phosphoribosyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.899 Å
AuthorsDonini, S. / 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: RCSB / 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 1.2Jan 10, 2024Group: 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.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: Orotate phosphoribosyltransferase
B: Orotate phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7773
Polymers40,6822
Non-polymers951
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-17 kcal/mol
Surface area14390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.262, 56.328, 59.470
Angle α, β, γ (deg.)90.00, 115.10, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 3 - 177 / Label seq-ID: 14 - 188

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Orotate phosphoribosyltransferase / OPRTase


Mass: 20340.977 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The overall electron density presents two gaps between the residues 1-2 and 97-104, 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: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.52 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 0.1M HEPES pH 7.5, 10% (w/v) PEG8000, 8% (v/v) Ethylene glycol, 1mM PRPP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.899→49.21 Å / Num. obs: 26990 / % possible obs: 99.1 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 13.6
Reflection shellResolution: 1.899→1.967 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.196 / Mean I/σ(I) obs: 4.78 / % possible all: 95.53

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
SCALAdata scaling
PHENIXmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HKI

5hki


Resolution: 1.899→53.85 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.891 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19506 1351 5 %RANDOM
Rwork0.15582 ---
obs0.15786 25624 98.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.702 Å2
Baniso -1Baniso -2Baniso -3
1--1.64 Å20 Å20.88 Å2
2---1.65 Å20 Å2
3---1.71 Å2
Refinement stepCycle: LAST / Resolution: 1.899→53.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2546 0 5 208 2759
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0192584
X-RAY DIFFRACTIONr_bond_other_d0.0070.022527
X-RAY DIFFRACTIONr_angle_refined_deg1.8281.9553509
X-RAY DIFFRACTIONr_angle_other_deg1.2735747
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7835336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.95221.622111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.45315406
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.521532
X-RAY DIFFRACTIONr_chiral_restr0.1030.2422
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022932
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02590
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_it2.5472.521359
X-RAY DIFFRACTIONr_mcbond_other2.5472.5171358
X-RAY DIFFRACTIONr_mcangle_it3.6043.7471690
X-RAY DIFFRACTIONr_mcangle_other3.6043.751691
X-RAY DIFFRACTIONr_scbond_it3.9133.1251225
X-RAY DIFFRACTIONr_scbond_other3.9123.1281226
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9694.4741820
X-RAY DIFFRACTIONr_long_range_B_refined7.71621.4092943
X-RAY DIFFRACTIONr_long_range_B_other7.64221.1222862
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 8742 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.15 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.899→1.948 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 84 -
Rwork0.192 1794 -
obs--94.09 %

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