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- PDB-8cag: Hypoxanthine-guanine phosphoribosyltransferase from E. coli -

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Basic information

Entry
Database: PDB / ID: 8cag
TitleHypoxanthine-guanine phosphoribosyltransferase from E. coli
ComponentsHypoxanthine phosphoribosyltransferase
KeywordsTRANSFERASE
Function / homology
Function and homology information


hypoxanthine phosphoribosyltransferase / guanine phosphoribosyltransferase activity / guanine salvage / hypoxanthine metabolic process / hypoxanthine phosphoribosyltransferase activity / GMP salvage / IMP salvage / purine ribonucleoside salvage / guanosine tetraphosphate binding / protein homotetramerization ...hypoxanthine phosphoribosyltransferase / guanine phosphoribosyltransferase activity / guanine salvage / hypoxanthine metabolic process / hypoxanthine phosphoribosyltransferase activity / GMP salvage / IMP salvage / purine ribonucleoside salvage / guanosine tetraphosphate binding / protein homotetramerization / magnesium ion binding / protein-containing complex / identical protein binding / cytosol
Similarity search - Function
Hypoxanthine phosphoribosyl transferase / : / Purine/pyrimidine phosphoribosyl transferases signature. / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain
Similarity search - Domain/homology
Hypoxanthine phosphoribosyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsTimofeev, V.I. / Shevtsov, M.B. / Abramchik, Y.A. / Kostromina, M.A. / Zayats, E.A. / Kuranova, I.P. / Esipov, R.S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Hypoxanthine-guanine phosphoribosyltransferase from E. coli
Authors: Timofeev, V.I. / Shevtsov, M.B. / Abramchik, Y.A. / Kostromina, M.A. / Zayats, E.A. / Kuranova, I.P. / Esipov, R.S.
History
DepositionJan 24, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypoxanthine phosphoribosyltransferase
B: Hypoxanthine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8434
Polymers39,7942
Non-polymers492
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-35 kcal/mol
Surface area15200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.650, 84.650, 167.242
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Hypoxanthine phosphoribosyltransferase / HPRT / 6-oxopurine phosphoribosyltransferase / 6-oxopurine PRTase


Mass: 19897.047 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: hpt, b0125, JW5009 / Production host: Escherichia coli (E. coli)
References: UniProt: P0A9M2, hypoxanthine phosphoribosyltransferase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 4.5 Å3/Da / Density % sol: 72.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS EIGER R 1M / Detector: PIXEL / Date: Sep 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 27430 / % possible obs: 98.81 % / Redundancy: 2.97 % / Rmerge(I) obs: 0.235 / Net I/σ(I): 2
Reflection shellResolution: 2.4→2.53 Å / Rmerge(I) obs: 0.29 / Num. unique obs: 3993

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Processing

Software
NameVersionClassification
REFMAC5refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→29.74 Å / Cor.coef. Fo:Fc: 0.89 / Cor.coef. Fo:Fc free: 0.854 / SU B: 9.56 / SU ML: 0.223 / Cross valid method: THROUGHOUT / ESU R: 0.265 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29283 1396 5.1 %RANDOM
Rwork0.25379 ---
obs0.25577 25994 98.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.077 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2--0.01 Å2-0 Å2
3----0.04 Å2
Refinement stepCycle: 1 / Resolution: 2.4→29.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2672 0 2 33 2707
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132728
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152699
X-RAY DIFFRACTIONr_angle_refined_deg1.6931.643679
X-RAY DIFFRACTIONr_angle_other_deg1.2151.5836212
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9755338
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.1420.805149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.73915515
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.521527
X-RAY DIFFRACTIONr_chiral_restr0.0680.2363
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022998
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02596
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_it3.9874.3681355
X-RAY DIFFRACTIONr_mcbond_other3.9784.3671354
X-RAY DIFFRACTIONr_mcangle_it6.0016.5271689
X-RAY DIFFRACTIONr_mcangle_other6.0026.5291690
X-RAY DIFFRACTIONr_scbond_it4.434.7791373
X-RAY DIFFRACTIONr_scbond_other4.4294.781374
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.7437.0111990
X-RAY DIFFRACTIONr_long_range_B_refined9.55250.0632828
X-RAY DIFFRACTIONr_long_range_B_other9.55250.0752828
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
Rfree0.321 109 -
Rwork0.291 1901 -
obs--99.8 %

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