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

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Basic information

Entry
Database: PDB / ID: 5lhu
TitleATP Phosphoribosyltransferase from Mycobacterium tuberculosis in complex with the allosteric inhibitor L-Histidine
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
HISTIDINE / ATP phosphoribosyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
Authorsde Chiara, C. / Pisco, J.P. / de Carvalho, L.P. / Smerdon, S.J. / Walker, P.A. / Ogrodowicz, R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
The Francis Crick Institute United Kingdom
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 1.0Jun 21, 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 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3Jan 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
Revision 1.4Oct 23, 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)32,5119
Polymers31,6861
Non-polymers8258
Water1,54986
1
A: ATP phosphoribosyltransferase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)195,06454
Polymers190,1166
Non-polymers4,94848
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 area26770 Å2
ΔGint-562 kcal/mol
Surface area71640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.012, 117.012, 127.332
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)
Strain: ATCC 25618 / H37Rv / Gene: hisG, Rv2121c, MTCY261.17c / Plasmid: pJ411 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold pLysS AG / References: UniProt: P9WMN1, ATP phosphoribosyltransferase
#2: Chemical ChemComp-HIS / HISTIDINE


Type: L-peptide linking / Mass: 156.162 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10N3O2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / 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.: 86 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.12 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 2.5 %(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: 2.02→47.08 Å / Num. obs: 22068 / % possible obs: 99.7 % / Redundancy: 4.8 % / Net I/σ(I): 22.3

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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: 2.02→42.444 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2345 1107 5.02 %
Rwork0.1936 --
obs0.1956 22068 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.02→42.444 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2143 0 47 86 2276
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072225
X-RAY DIFFRACTIONf_angle_d0.8533026
X-RAY DIFFRACTIONf_dihedral_angle_d15.4431340
X-RAY DIFFRACTIONf_chiral_restr0.058349
X-RAY DIFFRACTIONf_plane_restr0.005395
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.1120.29921510.25082579X-RAY DIFFRACTION100
2.112-2.22330.32791360.22812609X-RAY DIFFRACTION100
2.2233-2.36260.27441270.22662603X-RAY DIFFRACTION100
2.3626-2.5450.28261440.21922598X-RAY DIFFRACTION100
2.545-2.80110.27281370.22442601X-RAY DIFFRACTION100
2.8011-3.20630.25371420.21352633X-RAY DIFFRACTION100
3.2063-4.03910.23081360.19042648X-RAY DIFFRACTION100
4.0391-42.45340.19131340.16662690X-RAY DIFFRACTION98

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