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

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Basic information

Entry
Database: PDB / ID: 5hki
TitleCrystal structure of Mycobacterium tuberculosis H37Rv orotate phosphoribosyltransferase in complex with Fe(III) dicitrate
ComponentsOrotate phosphoribosyltransferase
KeywordsTRANSFERASE / OPRT / de novo pyrimidine nucleotide synthesis / ferric dicitrate 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
Iron(III) dicitrate / Orotate phosphoribosyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 1.2Jan 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
C: Orotate phosphoribosyltransferase
D: Orotate phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,6796
Polymers80,8114
Non-polymers8682
Water3,063170
1
A: Orotate phosphoribosyltransferase
B: Orotate phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8403
Polymers40,4062
Non-polymers4341
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-14 kcal/mol
Surface area14390 Å2
MethodPISA
2
C: Orotate phosphoribosyltransferase
D: Orotate phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8403
Polymers40,4062
Non-polymers4341
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-12 kcal/mol
Surface area14440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.421, 60.262, 65.181
Angle α, β, γ (deg.)85.64, 89.90, 79.96
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Orotate phosphoribosyltransferase / OPRTase


Mass: 20202.830 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: No His-tag was traced in this case. The overall electron density presents a gaps between the residues 1-3, numbered from the N-terminal methionine.
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-6ZJ / Iron(III) dicitrate


Mass: 434.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H10FeO14
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.67 Å3/Da / Density % sol: 54.04 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 0.01M Iron(III) chloride hexahydrate, 0.1M Sodium citrate tribasic dihydrate pH 6.1, 10% (v/v) Jeffamine M-600

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.4→42.17 Å / Num. obs: 18336 / % possible obs: 95.3 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 8.74
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.78 / % possible all: 94.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
SCALAdata scaling
ARPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2P1Z

2p1z


Resolution: 2.4→64.99 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.89 / SU B: 9.45 / SU ML: 0.213 / Cross valid method: THROUGHOUT / ESU R: 0.443 / ESU R Free: 0.283 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26015 1477 5.1 %RANDOM
Rwork0.19514 ---
obs0.19849 27688 95.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.789 Å2
Baniso -1Baniso -2Baniso -3
1--1.53 Å2-0.37 Å2-0 Å2
2--2.58 Å22.08 Å2
3----0.99 Å2
Refinement stepCycle: 1 / Resolution: 2.4→64.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5104 0 54 170 5328
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0195224
X-RAY DIFFRACTIONr_bond_other_d0.0020.025098
X-RAY DIFFRACTIONr_angle_refined_deg1.8431.9787118
X-RAY DIFFRACTIONr_angle_other_deg1.013311596
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3875680
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.57221.574216
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.03615832
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1561568
X-RAY DIFFRACTIONr_chiral_restr0.0880.2856
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025876
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021164
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_it2.4693.3922738
X-RAY DIFFRACTIONr_mcbond_other2.4573.3912737
X-RAY DIFFRACTIONr_mcangle_it3.8325.0733412
X-RAY DIFFRACTIONr_mcangle_other3.8315.0763413
X-RAY DIFFRACTIONr_scbond_it3.6743.8242486
X-RAY DIFFRACTIONr_scbond_other2.9363.7722427
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.635.5013597
X-RAY DIFFRACTIONr_long_range_B_refined6.74426.8055624
X-RAY DIFFRACTIONr_long_range_B_other6.60726.6715582
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 121 -
Rwork0.282 2012 -
obs--94.21 %

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