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- PDB-9k8m: Hypoxanthine-guanine phosphoribosyltransferase from E. coli with HEPES -

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Basic information

Entry
Database: PDB / ID: 9k8m
TitleHypoxanthine-guanine phosphoribosyltransferase from E. coli with HEPES
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 / nucleotide binding / magnesium ion 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: 2.08 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 with HEPES
Authors: Timofeev, V.I. / Shevtsov, M.B. / Abramchik, Y.A. / Kostromina, M.A. / Zayats, E.A. / Kuranova, I.P. / Esipov, R.S.
History
DepositionOct 24, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)40,2714
Polymers39,7942
Non-polymers4772
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-4 kcal/mol
Surface area15020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.217, 85.217, 168.279
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


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, c0154 / Production host: Escherichia coli (E. coli)
References: UniProt: P0A9M3, hypoxanthine phosphoribosyltransferase
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 4.43 Å3/Da / Density % sol: 72.25 %
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: ELETTRA / Beamline: 11.2C / Wavelength: 0.9999 Å
DetectorType: DECTRIS EIGER R 1M / Detector: PIXEL / Date: May 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.08→29.94 Å / Num. obs: 40751 / % possible obs: 99.67 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 8
Reflection shellResolution: 2.08→2.13 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.43 / Num. unique obs: 2877 / % possible all: 96.49

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.08→29.94 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.625 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22692 2109 4.9 %RANDOM
Rwork0.20396 ---
obs0.20509 40751 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.985 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.08→29.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2651 0 30 39 2720
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132748
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152730
X-RAY DIFFRACTIONr_angle_refined_deg1.9081.6443706
X-RAY DIFFRACTIONr_angle_other_deg1.41.5836290
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.735337
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.63620.667150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.15315517
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7531528
X-RAY DIFFRACTIONr_chiral_restr0.0790.2362
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022988
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_it4.4254.6591348
X-RAY DIFFRACTIONr_mcbond_other4.424.6581347
X-RAY DIFFRACTIONr_mcangle_it5.8956.9461682
X-RAY DIFFRACTIONr_mcangle_other5.8956.9481683
X-RAY DIFFRACTIONr_scbond_it5.6555.2351400
X-RAY DIFFRACTIONr_scbond_other5.6465.2361398
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.9587.6442024
X-RAY DIFFRACTIONr_long_range_B_refined9.21353.3842812
X-RAY DIFFRACTIONr_long_range_B_other9.21453.3722809
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.085→2.139 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 151 -
Rwork0.289 2877 -
obs--96.49 %

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