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- PDB-5bqp: Hypoxanthine-guanine-xanthine phosphoribosyltransferase (HGXPRT) ... -

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Basic information

Entry
Database: PDB / ID: 5bqp
TitleHypoxanthine-guanine-xanthine phosphoribosyltransferase (HGXPRT) from Sulfolobus solfataricus with xanthosine and phosphate bound in the nucleotide binding site and with sulfate bound in the pyrophosphate binding site
ComponentsPurine phosphoribosyltransferase (GpT-2)
KeywordsTRANSFERASE / HGXPRT / HGPRT / purine phosphoribosyltransferase
Function / homology
Function and homology information


glycosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases
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
2,3-dihydroxanthosine / TRIETHYLENE GLYCOL / PHOSPHATE ION / Purine phosphoribosyltransferase (GpT-2)
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsChristoffersen, S.
CitationJournal: to be published
Title: Sulfolobus solfataricus P2
Authors: Christoffersen, S. / Hansen, M.R. / Jensen, K.S. / Larsen, S. / Jensen, K.F.
History
DepositionMay 29, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1May 8, 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

Downloads & links

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Assembly

Deposited unit
A: Purine phosphoribosyltransferase (GpT-2)
B: Purine phosphoribosyltransferase (GpT-2)
C: Purine phosphoribosyltransferase (GpT-2)
D: Purine phosphoribosyltransferase (GpT-2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,54423
Polymers82,7284
Non-polymers2,81619
Water17,150952
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7890 Å2
ΔGint-131 kcal/mol
Surface area35130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.218, 132.218, 103.102
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Purine phosphoribosyltransferase (GpT-2)


Mass: 20682.057 Da / Num. of mol.: 4 / Fragment: hgxprt
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (archaea)
Gene: gpT-2, SSO2424 / Plasmid: pKU1 / Production host: Escherichia coli (E. coli) / Strain (production host): NF1830
References: UniProt: Q97W22, Transferases; Glycosyltransferases; Pentosyltransferases

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Non-polymers , 7 types, 971 molecules

#2: Chemical
ChemComp-4UO / 2,3-dihydroxanthosine / Xanthosine


Mass: 284.225 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H12N4O6
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 952 / Source method: isolated from a natural source / Formula: H2O

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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: 3.14 Å3/Da / Density % sol: 60.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 3.15 M ammonium sulfate, 0.1 M citric acid

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9771 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 20, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9771 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 114176 / Num. obs: 113561 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 3.54 % / Biso Wilson estimate: 18.74 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.071 / Rrim(I) all: 0.084 / Rsym value: 0.084 / Χ2: 0.974 / Net I/σ(I): 13.16 / Num. measured all: 401615
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.7-1.83.530.6820.6852.26433018338182030.8199.3
1.8-1.930.8610.4033.86057117211171190.47699.5
1.93-2.080.9490.226.575657416016159510.2699.6
2.08-2.280.9810.1310.295250214822147470.15499.5
2.28-2.550.9910.08314.654808113413133980.09899.9
2.55-2.940.9950.0619.284229711891118580.0799.7
2.94-3.60.9970.03927.623535510061100310.04699.7
3.6-5.070.9980.0334.8726881789578110.03698.9
5.070.9980.02735.7915024452944430.03398.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.7 Å47.01 Å
Translation1.7 Å47.01 Å

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASER2.5.6phasing
PHENIX1.9refinement
PDB_EXTRACT3.15data extraction
Coot0.8.1model building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→47.007 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1896 5678 5 %Random selection
Rwork0.1621 107861 --
obs0.1635 113539 99.45 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.75 Å2 / Biso mean: 27.1796 Å2 / Biso min: 7.79 Å2
Refinement stepCycle: final / Resolution: 1.7→47.007 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5562 0 178 952 6692
Biso mean--44.62 42.12 -
Num. residues----682
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135918
X-RAY DIFFRACTIONf_angle_d1.3838062
X-RAY DIFFRACTIONf_chiral_restr0.077926
X-RAY DIFFRACTIONf_plane_restr0.008965
X-RAY DIFFRACTIONf_dihedral_angle_d12.2422172
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6997-1.7190.28261820.28113460364297
1.719-1.73930.28031880.266335783766100
1.7393-1.76050.26591890.236735873776100
1.7605-1.78280.26241900.227136023792100
1.7828-1.80620.24841880.230335853773100
1.8062-1.8310.28411870.219735553742100
1.831-1.85710.24481890.214935813770100
1.8571-1.88480.24441880.20883578376699
1.8848-1.91430.22171880.2173561374999
1.9143-1.94570.26481880.2083579376799
1.9457-1.97920.2061870.187135493736100
1.9792-2.01520.18741890.175335983787100
2.0152-2.0540.20241890.183435783767100
2.054-2.09590.25991890.17873582377199
2.0959-2.14150.20171870.1735643751100
2.1415-2.19130.2261890.164535823771100
2.1913-2.24610.21641890.16653590377999
2.2461-2.30680.18781880.16173571375999
2.3068-2.37470.19791880.156835833771100
2.3747-2.45130.18651910.149836283819100
2.4513-2.5390.17881900.147736153805100
2.539-2.64060.18631900.149536003790100
2.6406-2.76080.16191890.15353601379099
2.7608-2.90630.18911910.152436113802100
2.9063-3.08840.17111910.147436333824100
3.0884-3.32680.1641910.138336333824100
3.3268-3.66140.17031910.13683636382799
3.6614-4.19090.14761910.12483627381899
4.1909-5.2790.141930.12913665385899
5.279-47.02470.19521980.18173749394798

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