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- PDB-4z1o: Hypoxanthine-guanine-xanthine phosphoribosyltransferase (HGXPRT) ... -

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Basic information

Entry
Database: PDB / ID: 4z1o
TitleHypoxanthine-guanine-xanthine phosphoribosyltransferase (HGXPRT) from Sulfolobus solfataricus in complex with alpha-phosphoribosylpyrophosphoric acid (PRPP) and Magnesium
ComponentsPhosphoribosyltransferase
KeywordsTRANSFERASE / phosphoribosyltransferase / HGXPRT / HGPRT
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
Chem-PRP / Phosphoribosyltransferase
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å
AuthorsChristoffersen, S.
CitationJournal: to be published
Title: Hypoxanthine-guanine-xanthine phosphoribosyltransferase (HGXPRT) from Sulfolobus solfataricus in complex with alpha-phosphoribosylpyrophosphoric acid (PRPP) and Magnesium
Authors: Christoffersen, S. / Hansen, M.R. / Jensen, K.S. / Larsen, S. / Jensen, K.F.
History
DepositionMar 27, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 29, 2015Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _atom_site.occupancy / _chem_comp.mon_nstd_flag ..._atom_site.occupancy / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoribosyltransferase
B: Phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1936
Polymers41,3642
Non-polymers8294
Water6,305350
1
A: Phosphoribosyltransferase
B: Phosphoribosyltransferase
hetero molecules

A: Phosphoribosyltransferase
B: Phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,38612
Polymers82,7284
Non-polymers1,6588
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area14510 Å2
ΔGint-134 kcal/mol
Surface area28470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.784, 73.784, 142.906
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11B-480-

HOH

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Components

#1: Protein Phosphoribosyltransferase


Mass: 20682.057 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Ordered Locus name SSO2424
Source: (gene. exp.) Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (archaea)
Strain: 98/2 / Gene: GpT-2 / Plasmid: pKU1 / Production host: Escherichia coli (E. coli) / Strain (production host): NF1830
References: UniProt: D0KMY9, hypoxanthine phosphoribosyltransferase
#2: Sugar ChemComp-PRP / 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose / ALPHA-PHOSPHORIBOSYLPYROPHOSPHORIC ACID / 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribose / 1-O-pyrophosphono-5-O-phosphono-D-ribose / 1-O-pyrophosphono-5-O-phosphono-ribose


Type: D-saccharide / Mass: 390.070 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H13O14P3
IdentifierTypeProgram
a-D-Ribf1PO35PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / 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: 2.35 Å3/Da / Density % sol: 47.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES, 15% PEG3350

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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: 2.15→50 Å / Num. all: 411125 / Num. obs: 22230 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 18.56 % / Biso Wilson estimate: 31.23 Å2 / Rmerge F obs: 0.996 / Rmerge(I) obs: 0.185 / Rrim(I) all: 0.191 / Χ2: 0.965 / Net I/σ(I): 12.35 / Num. measured all: 411125
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique allNum. unique obsRrim(I) all% possible all
2.15-2.280.8680.8673.12628503501343334330.89198.1
2.28-2.440.9510.6034.7266250331933180.618100
2.44-2.630.9770.4097.260910309530950.419100
2.63-2.880.9840.3059.9854591284028390.314100
2.88-3.220.9920.2091449750261826180.215100
3.22-3.720.9930.15919.3840769230723070.163100
3.72-4.540.9940.12923.7532977199819970.13499.9
4.54-6.390.9940.11526.3727537157715770.119100
6.390.9950.09327.03154919759670.09699.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.69 Å47.61 Å
Translation4.69 Å47.61 Å

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Processing

Software
NameVersionClassification
PHENIXrefinement
XDSdata reduction
PHASER2.5.2phasing
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
Coot0.7.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VDM

1vdm


Resolution: 2.15→42.136 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2787 1111 5.02 %Random selection
Rwork0.1886 21040 --
obs0.1932 22151 99.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.82 Å2 / Biso mean: 36.051 Å2 / Biso min: 10.08 Å2
Refinement stepCycle: final / Resolution: 2.15→42.136 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2839 0 46 350 3235
Biso mean--26.93 42.43 -
Num. residues----347
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082950
X-RAY DIFFRACTIONf_angle_d1.0314020
X-RAY DIFFRACTIONf_chiral_restr0.04462
X-RAY DIFFRACTIONf_plane_restr0.005485
X-RAY DIFFRACTIONf_dihedral_angle_d14.2991108
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1504-2.24830.34551320.27282516264898
2.2483-2.36680.31281370.230825822719100
2.3668-2.51510.30631360.2125922728100
2.5151-2.70930.33121370.21426022739100
2.7093-2.98180.30491380.202726152753100
2.9818-3.41320.27461390.182826292768100
3.4132-4.29950.26981410.157826672808100
4.2995-42.14420.23841510.17528372988100

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