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- PDB-4trb: Sulfolobus solfataricus adenine phosphoribosyltransferase -

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Basic information

Entry
Database: PDB / ID: 4trb
TitleSulfolobus solfataricus adenine phosphoribosyltransferase
ComponentsPurine phosphoribosyltransferase (GpT-1)
KeywordsTRANSFERASE / Sulfolobus / solfataricus / adenine / phosphoribosyltransferase
Function / homologyPhosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / glycosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / nucleotide binding / 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 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 1.4Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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)49,0366
Polymers48,6562
Non-polymers3804
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-39 kcal/mol
Surface area19240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.628, 125.628, 69.707
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 3:74 or resseq 76:169 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-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 66 / 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: 3.26 Å3/Da / Density % sol: 62.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Protein: 6.2 mg/mL, 25 mM TRIS pH 7.6, 0.1 mM EDTA, Buffer: 0.1 M MES pH 6.5, Precipitant: 30 % Jeffamine M-600

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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: CCD / 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: 24914 / % possible obs: 100 % / Redundancy: 8.2 % / Net I/σ(I): 23.8

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.5_2) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NUL and 1VDM

1nul

1vdm


Resolution: 2.4→19.721 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2865 1232 5.01 %
Rwork0.2278 --
obs0.2306 24602 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.189 Å2 / ksol: 0.338 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.5025 Å20 Å20 Å2
2---8.5025 Å2-0 Å2
3---17.005 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.721 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3416 0 20 66 3502
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083506
X-RAY DIFFRACTIONf_angle_d0.9854770
X-RAY DIFFRACTIONf_dihedral_angle_d16.9471296
X-RAY DIFFRACTIONf_chiral_restr0.064552
X-RAY DIFFRACTIONf_plane_restr0.005588
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1628X-RAY DIFFRACTIONPOSITIONAL
12B1628X-RAY DIFFRACTIONPOSITIONAL0.063
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.4960.39761340.29962580X-RAY DIFFRACTION100
2.496-2.60930.39921400.28752585X-RAY DIFFRACTION100
2.6093-2.74660.33841300.27822587X-RAY DIFFRACTION100
2.7466-2.91810.37521390.28122579X-RAY DIFFRACTION100
2.9181-3.14260.35991390.27412590X-RAY DIFFRACTION100
3.1426-3.45730.34271410.27112584X-RAY DIFFRACTION100
3.4573-3.95410.27671320.22912591X-RAY DIFFRACTION100
3.9541-4.96850.2251380.18752634X-RAY DIFFRACTION100
4.9685-19.72140.20181390.16282640X-RAY DIFFRACTION99

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