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- PDB-4trc: Sulfolobus solfataricus adenine phosphoribosyltransferase with adenine -

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Basic information

Entry
Database: PDB / ID: 4trc
TitleSulfolobus solfataricus adenine phosphoribosyltransferase with adenine
ComponentsPurine phosphoribosyltransferase (GpT-1)
KeywordsTRANSFERASE / Sulfolobus / solfataricus / adenine / phosphoribosyltransferase
Function / homologyPhosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / glycosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / nucleotide binding / ADENINE / PHOSPHATE ION / Purine phosphoribosyltransferase (GpT-1)
Function and homology information
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 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 16, 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 1.4Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Feb 14, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.pdbx_collection_date
Revision 1.6May 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-1)
B: Purine phosphoribosyltransferase (GpT-1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4029
Polymers48,6562
Non-polymers7457
Water2,828157
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5560 Å2
ΔGint-41 kcal/mol
Surface area19810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.200, 137.200, 53.800
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 301:303 )
211chain B and (resseq 2:6 or resseq 8:112 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) / Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: gpT-1, SSO2342 / Production host: Escherichia coli (E. coli)
References: UniProt: Q97W95, Transferases; Glycosyltransferases; Pentosyltransferases
#2: Chemical ChemComp-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H5N5
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 3 Å3/Da / Density % sol: 59.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Protein 8.9 mg/mL 25 mM TRIS pH 7.6 0.1 mM EDTA 5 mM adenine Buffer 0.1 M phosphate-citrate pH 4.2 Precipitant 20 % PEG1000 0.2 M Li2SO4

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Data collection

DiffractionMean temperature: 122 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.03911 Å
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Apr 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03911 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 22808 / % possible obs: 99.6 % / Redundancy: 13.6 % / Net I/σ(I): 28.26

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.5_2) / Classification: refinement
RefinementResolution: 2.4→29.705 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2416 1146 5.03 %
Rwork0.2001 --
obs0.2022 22795 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.456 Å2 / ksol: 0.351 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.4065 Å2-0 Å20 Å2
2---0.4065 Å2-0 Å2
3---0.813 Å2
Refinement stepCycle: LAST / Resolution: 2.4→29.705 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3416 0 45 157 3618
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083532
X-RAY DIFFRACTIONf_angle_d0.9824806
X-RAY DIFFRACTIONf_dihedral_angle_d17.4241296
X-RAY DIFFRACTIONf_chiral_restr0.064552
X-RAY DIFFRACTIONf_plane_restr0.005590
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1561X-RAY DIFFRACTIONPOSITIONAL
12B1561X-RAY DIFFRACTIONPOSITIONAL0.051
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.50920.33671380.24162683X-RAY DIFFRACTION100
2.5092-2.64140.27071490.22962719X-RAY DIFFRACTION100
2.6414-2.80680.26291370.2312680X-RAY DIFFRACTION100
2.8068-3.02330.2941430.23612711X-RAY DIFFRACTION100
3.0233-3.32720.27261440.22552690X-RAY DIFFRACTION100
3.3272-3.80780.24621440.19932679X-RAY DIFFRACTION98
3.8078-4.79410.18811430.152716X-RAY DIFFRACTION100
4.7941-29.70690.17541480.15352771X-RAY DIFFRACTION99

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