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- PDB-4ts7: Sulfolobus solfataricus adenine phosphoribosyltransferase with ADP -

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Basic information

Entry
Database: PDB / ID: 4ts7
TitleSulfolobus solfataricus adenine phosphoribosyltransferase with ADP
ComponentsPurine phosphoribosyltransferase (GpT-1)
KeywordsTRANSFERASE
Function / homologyPhosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / glycosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / nucleotide binding / ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / Purine phosphoribosyltransferase (GpT-1)
Function and homology information
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsKadziola, A.
CitationJournal: Biochemistry / Year: 2015
Title: Adenine Phosphoribosyltransferase from Sulfolobus solfataricus Is an Enzyme with Unusual Kinetic Properties and a Crystal Structure that Suggests It Evolved from a 6-Oxopurine Phosphoribosyltransferase.
Authors: Jensen, K.F. / Hansen, M.R. / Jensen, K.S. / Christoffersen, S. / Poulsen, J.C. / Mlgaard, A. / Kadziola, A.
History
DepositionJun 18, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2015Group: Database references
Revision 1.2Apr 8, 2015Group: Database references
Revision 1.3Apr 22, 2015Group: Database references
Revision 1.4Feb 14, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.pdbx_collection_date
Revision 1.5May 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

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Assembly

Deposited unit
A: Purine phosphoribosyltransferase (GpT-1)
B: Purine phosphoribosyltransferase (GpT-1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7967
Polymers48,6562
Non-polymers1,1395
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5850 Å2
ΔGint-43 kcal/mol
Surface area19560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.716, 135.716, 54.151
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 2:210 or resseq 301:302 )
211chain B and (resseq 4:6 or resseq 8:107 or resseq...

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Components

#1: Protein Purine phosphoribosyltransferase (GpT-1)


Mass: 24328.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Production host: Escherichia coli (E. coli)
References: UniProt: Q97W95, Transferases; Glycosyltransferases; Pentosyltransferases
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 58.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Protein 14 mg/mL 25 mM TRIS pH 7.6 0.1 mM EDTA 10 mM Mg(NO3)2 10 mM ATP Buffer 0.1 M bis-TRIS pH 5.5 Precipitant 21 % PEG3350 0.2 M Li2SO4

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Data collection

DiffractionMean temperature: 122 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Feb 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 14393 / % possible obs: 100 % / Redundancy: 8.6 % / Rmerge(I) obs: 0.145 / Net I/σ(I): 18.3
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 5 / % possible all: 99.9

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.5_2) / Classification: refinement
RefinementResolution: 2.8→19.911 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2215 717 5.05 %
Rwork0.1722 --
obs0.1747 14212 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 14.742 Å2 / ksol: 0.327 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.2374 Å20 Å20 Å2
2---2.2374 Å2-0 Å2
3---4.4747 Å2
Refinement stepCycle: LAST / Resolution: 2.8→19.911 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3416 0 69 85 3570
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083560
X-RAY DIFFRACTIONf_angle_d1.1514854
X-RAY DIFFRACTIONf_dihedral_angle_d18.9981318
X-RAY DIFFRACTIONf_chiral_restr0.076560
X-RAY DIFFRACTIONf_plane_restr0.004590
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1577X-RAY DIFFRACTIONPOSITIONAL
12B1577X-RAY DIFFRACTIONPOSITIONAL0.045
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8001-3.01570.30021420.22092676X-RAY DIFFRACTION100
3.0157-3.31790.27651420.20392672X-RAY DIFFRACTION100
3.3179-3.79510.21341430.17262672X-RAY DIFFRACTION100
3.7951-4.77050.19081380.13422707X-RAY DIFFRACTION100
4.7705-19.91170.16251520.1442768X-RAY DIFFRACTION100

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