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- PDB-5lht: ATP Phosphoribosyltransferase from Mycobacterium tuberculosis in ... -

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Basic information

Entry
Database: PDB / ID: 5lht
TitleATP Phosphoribosyltransferase from Mycobacterium tuberculosis in complex with the allosteric activator 3-(2-Thienyl)-L-alanine
ComponentsATP phosphoribosyltransferase
KeywordsTRANSFERASE / ATP-PRTase / ACT / His G / Histidine biosynthesis
Function / homology
Function and homology information


ATP phosphoribosyltransferase / ATP phosphoribosyltransferase activity / L-histidine biosynthetic process / AMP binding / magnesium ion binding / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
ATP phosphoribosyltransferase HisG, long form / Histidine biosynthesis HisG, C-terminal / HisG, C-terminal domain / ATP phosphoribosyltransferase HisG / ATP phosphoribosyltransferase, catalytic domain / ATP phosphoribosyltransferase, conserved site / ATP phosphoribosyltransferase / ATP phosphoribosyltransferase signature. / Alpha-Beta Plaits - #120 / Nitrogen regulatory PII-like, alpha/beta ...ATP phosphoribosyltransferase HisG, long form / Histidine biosynthesis HisG, C-terminal / HisG, C-terminal domain / ATP phosphoribosyltransferase HisG / ATP phosphoribosyltransferase, catalytic domain / ATP phosphoribosyltransferase, conserved site / ATP phosphoribosyltransferase / ATP phosphoribosyltransferase signature. / Alpha-Beta Plaits - #120 / Nitrogen regulatory PII-like, alpha/beta / Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BETA(2-THIENYL)ALANINE / ATP phosphoribosyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.0601 Å
Authorsde Chiara, C. / Pisco, J.P. / de Carvalho, L.P. / Smerdon, S.J. / Walker, P.A. / Ogrodowicz, R.
Citation
Journal: Nat Commun / Year: 2017
Title: Uncoupling conformational states from activity in an allosteric enzyme.
Authors: Pisco, J.P. / Chiara, C. / Pacholarz, K.J. / Garza-Garcia, A. / Ogrodowicz, R.W. / Walker, P.A. / Barran, P.E. / Smerdon, S.J. / Carvalho, L.P.S.
#1: Journal: Biochemistry / Year: 2012
Title: Mechanism of feedback allosteric inhibition of ATP phosphoribosyltransferase.
Authors: Pedreno, S. / Pisco, J.P. / Larrouy-Maumus, G. / Kelly, G. / de Carvalho, L.P.
History
DepositionJul 12, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_high / _refine_hist.d_res_low
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3347
Polymers31,6861
Non-polymers6486
Water1,47782
1
A: ATP phosphoribosyltransferase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)194,00242
Polymers190,1166
Non-polymers3,88536
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_557y,x,-z+21
crystal symmetry operation5_557x-y,-y,-z+21
crystal symmetry operation6_557-x,-x+y,-z+21
Buried area23900 Å2
ΔGint-393 kcal/mol
Surface area72180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.512, 117.512, 127.356
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein ATP phosphoribosyltransferase / ATP-PRTase


Mass: 31686.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Gene: hisG, Rv2121c, MTCY261.17c / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold pLysS AG / References: UniProt: P9WMN1, ATP phosphoribosyltransferase
#2: Chemical ChemComp-TIH / BETA(2-THIENYL)ALANINE


Type: L-peptide linking / Mass: 171.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H9NO2S
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.7855.69
22.7855.69
Crystal grow
Temperature (K)Crystal-IDMethodDetails
291.151vapor diffusion, sitting drop2.5 %(v/v) Isopropanol, 1.0 M Ammonium sulfate
291.152vapor diffusion, sitting drop2.5 %(v/v) Isopropanol, 1.0 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 2.0609→47.2522 Å / Num. obs: 20991 / % possible obs: 99.7 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 16.1
Reflection shellRmerge(I) obs: 0.69

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NH8

1nh8


Resolution: 2.0601→47.2522 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2285 1016 4.84 %
Rwork0.1926 --
obs0.1943 20990 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.0601→47.2522 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2143 0 37 82 2262
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082223
X-RAY DIFFRACTIONf_angle_d0.8973024
X-RAY DIFFRACTIONf_dihedral_angle_d14.5391342
X-RAY DIFFRACTIONf_chiral_restr0.057350
X-RAY DIFFRACTIONf_plane_restr0.005397
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0601-2.16870.31161440.24992830X-RAY DIFFRACTION100
2.1687-2.30460.29711600.23352805X-RAY DIFFRACTION100
2.3046-2.48250.28241390.22072842X-RAY DIFFRACTION100
2.4825-2.73230.29581430.21922845X-RAY DIFFRACTION100
2.7323-3.12760.26991390.21642839X-RAY DIFFRACTION100
3.1276-3.94020.21951440.19082884X-RAY DIFFRACTION100
3.9402-47.26460.18321470.16742929X-RAY DIFFRACTION99

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