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- PDB-7kl6: Helicobacter pylori Xanthine-Guanine-Hypoxanthine Phosphoribosylt... -

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Basic information

Entry
Database: PDB / ID: 7kl6
TitleHelicobacter pylori Xanthine-Guanine-Hypoxanthine Phosphoribosyltransferase
ComponentsPhosphoribosyltransferase
KeywordsTRANSFERASE / Helicobacter pylori Xanthine-Guanine-Hypoxanthine Phosphoribosyltransferase Drug discovery Nucleoside phosphonates
Function / homology
Function and homology information


glycosyltransferase activity
Similarity search - Function
Rossmann fold - #2020 / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-WG7 / Phosphoribosyltransferase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.97 Å
AuthorsGuddat, L.W. / Keough, D.T.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: J.Med.Chem. / Year: 2021
Title: Helicobacter pylori Xanthine-Guanine-Hypoxanthine Phosphoribosyltransferase-A Putative Target for Drug Discovery against Gastrointestinal Tract Infections.
Authors: Keough, D.T. / Wun, S.J. / Baszczynski, O. / Eng, W.S. / Spacek, P. / Panjikar, S. / Naesens, L. / Pohl, R. / Rejman, D. / Hockova, D. / Ferrero, R.L. / Guddat, L.W.
History
DepositionOct 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1May 26, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _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: Phosphoribosyltransferase
B: Phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5996
Polymers37,0242
Non-polymers5744
Water6,017334
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-68 kcal/mol
Surface area13240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.221, 51.488, 82.879
Angle α, β, γ (deg.)90.000, 96.214, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Phosphoribosyltransferase / Xanthine-Guanine-Hypoxanthine Phosphoribosyltransferase


Mass: 18512.184 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: BXP09_04485, CV723_04510 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A2L2I2A6, Transferases; Glycosyltransferases
#2: Chemical ChemComp-WG7 / (3-{[(4-oxo-4,5-dihydro-3H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]amino}propyl)phosphonic acid


Mass: 286.224 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N4O4P
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.3 Å3/Da / Density % sol: 46.62 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-Tris propane, pH 5.5, 0.2 M ammonium sulfate, 25 % PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1.3776 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Oct 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3776 Å / Relative weight: 1
ReflectionResolution: 1.96→43.78 Å / Num. obs: 24376 / % possible obs: 99.5 % / Redundancy: 14 % / Biso Wilson estimate: 17.02 Å2 / CC1/2: 0.8 / Net I/σ(I): 74.96
Reflection shellResolution: 1.96→2.08 Å / Num. unique obs: 2370 / CC1/2: 0.6

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Processing

Software
NameVersionClassification
Auto-Rickshaw1.18.2_3874refinement
PHENIX1.18.2_3874refinement
ARP/wARPdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MIR / Resolution: 1.97→19.99 Å / SU ML: 0.1593 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 17.6193
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1926 893 3.93 %
Rwork0.1608 21811 -
obs0.162 22704 94.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.35 Å2
Refinement stepCycle: LAST / Resolution: 1.97→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2348 0 34 334 2716
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00982470
X-RAY DIFFRACTIONf_angle_d1.20173354
X-RAY DIFFRACTIONf_chiral_restr0.0648375
X-RAY DIFFRACTIONf_plane_restr0.0069413
X-RAY DIFFRACTIONf_dihedral_angle_d11.4807322
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.090.19571510.16623482X-RAY DIFFRACTION91.95
2.09-2.260.21591360.15943569X-RAY DIFFRACTION93.14
2.26-2.480.18121430.16213541X-RAY DIFFRACTION93.12
2.48-2.840.19621630.16993699X-RAY DIFFRACTION96.48
2.84-3.580.20541380.15623681X-RAY DIFFRACTION95.71
3.58-19.990.17991620.15833839X-RAY DIFFRACTION97.85
Refinement TLS params.Method: refined / Origin x: 28.2602522598 Å / Origin y: 6.1153507424 Å / Origin z: 103.375020692 Å
111213212223313233
T0.0944883088341 Å20.00289376183946 Å2-0.0160765677574 Å2-0.0823596548783 Å20.00955625695351 Å2--0.0804064194932 Å2
L1.20325713389 °2-0.0931832341492 °2-0.43800175753 °2-0.855581546311 °20.123439987442 °2--1.58172739213 °2
S0.0241372477571 Å °0.124143421176 Å °0.0360715994209 Å °-0.0244586426933 Å °-0.00524738275746 Å °-0.00344655400165 Å °0.00966876179623 Å °-0.027441420976 Å °-0.00943452914624 Å °
Refinement TLS groupSelection details: all

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