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- PDB-4ts5: Sulfolobus solfataricus adenine phosphoribosyltransferase with AMP -

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Basic information

Entry
Database: PDB / ID: 4ts5
TitleSulfolobus solfataricus adenine phosphoribosyltransferase with AMP
ComponentsPurine phosphoribosyltransferase (GpT-1)
KeywordsTRANSFERASE
Function / homologyPhosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / glycosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / nucleotide binding / ADENOSINE MONOPHOSPHATE / PHOSPHATE ION / Purine phosphoribosyltransferase (GpT-1)
Function and homology information
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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 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

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)49,6367
Polymers48,6562
Non-polymers9795
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5630 Å2
ΔGint-34 kcal/mol
Surface area19920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.648, 134.648, 53.081
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 2:170 or resseq 178:178 or resseq...

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Components

#1: Protein Purine phosphoribosyltransferase (GpT-1) / Sulfolobus solfataricus adenine phosphoribosyltransferase


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-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*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.: 156 / 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: 2.85 Å3/Da / Density % sol: 56.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Protein 14 mg/mL 25 mM TRIS pH 7.6 0.1 mM EDTA 5 mM MgCl2 2mM AMP Buffer 0.1 M SPG pH 4.0 Precipitant 25 % PEG1500

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Data collection

DiffractionMean temperature: 122 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Feb 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 22064 / % possible obs: 99.9 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 21.7
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 3.4 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.5_2)phasing
PHENIX(phenix.refine: 1.5_2)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→19.625 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2423 1087 5.01 %
Rwork0.19 --
obs0.1925 21679 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.646 Å2 / ksol: 0.373 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.1516 Å20 Å20 Å2
2---5.1516 Å2-0 Å2
3---10.3032 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.625 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3416 0 61 156 3633
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073552
X-RAY DIFFRACTIONf_angle_d1.064840
X-RAY DIFFRACTIONf_dihedral_angle_d16.9861314
X-RAY DIFFRACTIONf_chiral_restr0.069560
X-RAY DIFFRACTIONf_plane_restr0.005590
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1624X-RAY DIFFRACTIONPOSITIONAL
12B1624X-RAY DIFFRACTIONPOSITIONAL0.05
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.50920.27791320.22092535X-RAY DIFFRACTION100
2.5092-2.64110.281190.21762600X-RAY DIFFRACTION100
2.6411-2.80620.25931410.21942526X-RAY DIFFRACTION100
2.8062-3.02210.29031340.21792558X-RAY DIFFRACTION100
3.0221-3.32490.25951390.20682556X-RAY DIFFRACTION100
3.3249-3.8030.24881390.18342580X-RAY DIFFRACTION100
3.803-4.77990.19611300.15512598X-RAY DIFFRACTION100
4.7799-19.62610.20671530.16132639X-RAY DIFFRACTION100

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