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- PDB-6fsp: Crystal structure of APRT from Thermus thermophilus -

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Basic information

Entry
Database: PDB / ID: 6fsp
TitleCrystal structure of APRT from Thermus thermophilus
ComponentsPRPP-binding protein, adenine/guanine phosphoribosyltransferase
KeywordsTRANSFERASE
Function / homology
Function and homology information


glycosyltransferase activity
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
PRPP-binding protein, adenine/guanine phosphoribosyltransferase / Adenine phosphoribosyltransferase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å
AuthorsTimofeev, V.I. / Sinitsyna, E.V. / Kostromina, M.A. / Muravieva, T.I. / Makarov, D.A. / Mikheeva, O.O. / Kuranova, I.P. / Esipov, R.S.
CitationJournal: To Be Published
Title: Crystal structure of APRT from Thermus thermophilus
Authors: Timofeev, V.I. / Sinitsyna, E.V. / Kostromina, M.A. / Muravieva, T.I. / Makarov, D.A. / Mikheeva, O.O. / Kuranova, I.P. / Esipov, R.S.
History
DepositionFeb 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2019Provider: 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: PRPP-binding protein, adenine/guanine phosphoribosyltransferase
B: PRPP-binding protein, adenine/guanine phosphoribosyltransferase
C: PRPP-binding protein, adenine/guanine phosphoribosyltransferase
D: PRPP-binding protein, adenine/guanine phosphoribosyltransferase
E: PRPP-binding protein, adenine/guanine phosphoribosyltransferase
F: PRPP-binding protein, adenine/guanine phosphoribosyltransferase


Theoretical massNumber of molelcules
Total (without water)110,5536
Polymers110,5536
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13000 Å2
ΔGint-40 kcal/mol
Surface area42350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.860, 82.160, 91.390
Angle α, β, γ (deg.)90.00, 102.58, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
PRPP-binding protein, adenine/guanine phosphoribosyltransferase


Mass: 18425.527 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: TYPVEIAGVRRELPIVQVGPGVAVALLNLLGDTELTEAAAEALAKRLPPEVEVLVTPEVKAVPLAHALSRITGKPYVVARKTEKPYMINPVSRQVLSITTGKPQLLVLDGADIPRVRGKKVAIVDDVVSTGSTLAGLRELIESVGGEVVAVLAVFTEGTPRQDVVALGHLP
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: TtJL18_0431 / Production host: Escherichia coli (E. coli) / References: UniProt: H9ZPT0, UniProt: Q5SHW6*PLUS

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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: 2.33 Å3/Da / Density % sol: 47.2 %
Crystal growTemperature: 296 K / Method: liquid diffusion / Details: SA 25%

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.8 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 25557 / % possible obs: 96.6 % / Redundancy: 3.4 % / Net I/σ(I): 15.24
Reflection shellResolution: 2.7→2.77 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.85 / Cor.coef. Fo:Fc free: 0.77 / SU B: 50.631 / SU ML: 0.483 / Cross valid method: THROUGHOUT / ESU R Free: 0.556 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27118 1354 5 %RANDOM
Rwork0.24812 ---
obs0.23567 25506 96.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 46.147 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å2-0.43 Å2
2---0.77 Å2-0 Å2
3---0.6 Å2
Refinement stepCycle: 1 / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7731 0 0 0 7731
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0197849
X-RAY DIFFRACTIONr_bond_other_d0.0020.028071
X-RAY DIFFRACTIONr_angle_refined_deg1.7542.01710734
X-RAY DIFFRACTIONr_angle_other_deg1.177318626
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.92151033
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.78523.333255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.576151329
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9061565
X-RAY DIFFRACTIONr_chiral_restr0.1120.21373
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0218542
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021355
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0823.4834150
X-RAY DIFFRACTIONr_mcbond_other2.0833.4844149
X-RAY DIFFRACTIONr_mcangle_it3.6885.2175177
X-RAY DIFFRACTIONr_mcangle_other3.6875.2175178
X-RAY DIFFRACTIONr_scbond_it1.3643.6283699
X-RAY DIFFRACTIONr_scbond_other1.3643.6273700
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4925.4035558
X-RAY DIFFRACTIONr_long_range_B_refined8.5263.8729672
X-RAY DIFFRACTIONr_long_range_B_other8.5263.86929672
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.43 87 -
Rwork0.297 1880 -
obs--98.01 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.11720.3908-1.00040.56820.33692.1203-0.01060.17610.08330.05220.0340.01670.1352-0.1618-0.02340.05020.0619-0.0140.1377-0.01710.073855.657-0.9793122.5783
20.2993-0.1843-0.58340.28640.42731.18450.0501-0.07990.03080.02240.0466-0.0437-0.05930.2111-0.09670.060.0413-0.00880.1788-0.07530.055166.11277.4096140.3621
31.5646-0.8131-0.33060.7779-0.08680.7636-0.01070.22690.2841-0.0992-0.0378-0.0920.0189-0.05330.04850.0383-0.0214-0.03270.22240.11950.119685.38234.274792.514
41.7467-0.3299-0.10250.88280.18031.1155-0.1238-0.02940.1658-0.04350.1121-0.02970.0325-0.09760.01170.03230.00420.01020.08670.01470.043291.8702-6.8597110.8439
50.34620.1412-0.6161.4145-0.05761.6442-0.08540.0528-0.18240.0188-0.09660.1450.0241-0.07460.18190.0568-0.04480.08410.0971-0.02560.200137.9309-12.6901158.9589
61.1366-0.1756-0.79280.8068-0.21340.70010.0275-0.0080.00960.09510.02610.1325-0.0478-0.0132-0.05370.0837-0.04840.06540.1012-0.00910.063532.55767.6749166.4345
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 175
2X-RAY DIFFRACTION2B2 - 175
3X-RAY DIFFRACTION3C3 - 173
4X-RAY DIFFRACTION4D2 - 175
5X-RAY DIFFRACTION5E2 - 175
6X-RAY DIFFRACTION6F2 - 173

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