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- PDB-5bqo: Hypoxanthine-guanine-xanthine phosphoribosyltransferase (HGXPRT) ... -

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Basic information

Entry
Database: PDB / ID: 5bqo
TitleHypoxanthine-guanine-xanthine phosphoribosyltransferase (HGXPRT) from Sulfolobus solfataricus with sulfate bound in the 5-phosphoribosyl binding site.
ComponentsPurine phosphoribosyltransferase (GpT-2)
KeywordsTRANSFERASE / HGXPRT / HGPRT / purine phosphoribosyltransferase
Function / homology
Function and homology information


glycosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases
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
Purine phosphoribosyltransferase (GpT-2)
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.394 Å
AuthorsChristoffersen, S.
CitationJournal: to be published
Title: Sulfolobus solfataricus P2
Authors: Christoffersen, S. / Hansen, M.R. / Jensen, K.S. / Larsen, S. / Jensen, K.F.
History
DepositionMay 29, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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-2)
B: Purine phosphoribosyltransferase (GpT-2)
C: Purine phosphoribosyltransferase (GpT-2)
D: Purine phosphoribosyltransferase (GpT-2)
E: Purine phosphoribosyltransferase (GpT-2)
F: Purine phosphoribosyltransferase (GpT-2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,76513
Polymers124,0926
Non-polymers6727
Water11,800655
1
A: Purine phosphoribosyltransferase (GpT-2)
B: Purine phosphoribosyltransferase (GpT-2)
hetero molecules

A: Purine phosphoribosyltransferase (GpT-2)
B: Purine phosphoribosyltransferase (GpT-2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,30510
Polymers82,7284
Non-polymers5766
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area12950 Å2
ΔGint-167 kcal/mol
Surface area29850 Å2
MethodPISA
2
C: Purine phosphoribosyltransferase (GpT-2)
D: Purine phosphoribosyltransferase (GpT-2)
E: Purine phosphoribosyltransferase (GpT-2)
F: Purine phosphoribosyltransferase (GpT-2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,1128
Polymers82,7284
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12400 Å2
ΔGint-124 kcal/mol
Surface area30450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.946, 175.366, 151.784
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-310-

HOH

21A-411-

HOH

31A-425-

HOH

41B-364-

HOH

51F-388-

HOH

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Components

#1: Protein
Purine phosphoribosyltransferase (GpT-2) / hgxprt


Mass: 20682.057 Da / Num. of mol.: 6 / Fragment: hgxprt, UNP residues 1-179
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (archaea)
Gene: gpT-2, SSO2424 / Plasmid: pKU1 / Production host: Escherichia coli K-12 (bacteria)
References: UniProt: Q97W22, hypoxanthine phosphoribosyltransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 655 / Source method: isolated from a natural source / Formula: H2O

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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: 2.74 Å3/Da / Density % sol: 55.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 0.8 M ammonium sulfate, 0.1 M citric acid

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 30, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9395 Å / Relative weight: 1
ReflectionResolution: 2.39→50 Å / Num. all: 53296 / Num. obs: 52739 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 8.8 % / Biso Wilson estimate: 47.83 Å2 / Rmerge F obs: 0.995 / Rmerge(I) obs: 0.151 / Rrim(I) all: 0.16 / Rsym value: 0.16 / Χ2: 1.015 / Net I/σ(I): 9.49 / Num. measured all: 464194
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.39-2.540.8810.7781.9369087853280180.82694
2.54-2.710.920.5593.0373426797579750.592100
2.71-2.930.9540.3944.6469200748374820.417100
2.93-3.210.9740.2627.8362969687168700.278100
3.21-3.590.9850.17611.9855746627262700.187100
3.59-4.140.9940.12716.1646823554255400.135100
4.14-5.060.9910.10519.2838583475047470.11299.9
5.06-7.110.9920.09619.1230480367336700.10399.9
7.110.9950.07721.1817879219821660.08298.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.4 Å47.99 Å
Translation2.4 Å47.99 Å

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Processing

Software
NameVersionClassification
PHENIX1.9refinement
XSCALEdata scaling
PHASER2.5.6phasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
Coot0.8.1model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZFN

4zfn


Resolution: 2.394→47.991 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2507 2635 5 %Random selection
Rwork0.1914 50070 --
obs0.1944 52705 98.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.64 Å2 / Biso mean: 54.2489 Å2 / Biso min: 20.76 Å2
Refinement stepCycle: final / Resolution: 2.394→47.991 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8464 0 35 655 9154
Biso mean--74.82 58.46 -
Num. residues----1037
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028692
X-RAY DIFFRACTIONf_angle_d0.58611826
X-RAY DIFFRACTIONf_chiral_restr0.0221362
X-RAY DIFFRACTIONf_plane_restr0.0031445
X-RAY DIFFRACTIONf_dihedral_angle_d11.873213
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3944-2.4380.39361140.3662151226581
2.438-2.48490.36761370.277226092746100
2.4849-2.53560.36331400.273926522792100
2.5356-2.59070.35741380.254726152753100
2.5907-2.6510.32981400.251926672807100
2.651-2.71730.29241380.252926122750100
2.7173-2.79070.3311380.24926312769100
2.7907-2.87280.36321400.242626692809100
2.8728-2.96550.30371390.238526372776100
2.9655-3.07150.341390.223726402779100
3.0715-3.19450.26611390.214426382777100
3.1945-3.33980.29421400.196626492789100
3.3398-3.51590.23251410.188726842825100
3.5159-3.73610.24351390.175226502789100
3.7361-4.02440.20261410.16126692810100
4.0244-4.42910.21321400.153126702810100
4.4291-5.06940.21631440.152327202864100
5.0694-6.38460.23371420.18627022844100
6.3846-48.00050.1871460.16692805295199

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