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- PDB-2jkz: SACCHAROMYCES CEREVISIAE HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANS... -

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Basic information

Entry
Database: PDB / ID: 2jkz
TitleSACCHAROMYCES CEREVISIAE HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE IN COMPLEX WITH GMP (GUANOSINE 5'- MONOPHOSPHATE) (ORTHORHOMBIC CRYSTAL FORM)
ComponentsHYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE
KeywordsTRANSFERASE / NUCLEUS / CYTOPLASM / MAGNESIUM / GMP COMPLEX / FLIP PEPTIDE-PLANE / GLYCOSYLTRANSFERASE / METAL-BINDING / PURINE SALVAGE
Function / homology
Function and homology information


XMP salvage / hypoxanthine phosphoribosyltransferase / guanine phosphoribosyltransferase activity / hypoxanthine metabolic process / hypoxanthine phosphoribosyltransferase activity / GMP salvage / IMP salvage / purine ribonucleoside salvage / nucleotide binding / nucleus ...XMP salvage / hypoxanthine phosphoribosyltransferase / guanine phosphoribosyltransferase activity / hypoxanthine metabolic process / hypoxanthine phosphoribosyltransferase activity / GMP salvage / IMP salvage / purine ribonucleoside salvage / nucleotide binding / nucleus / metal ion binding / cytoplasm
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
GUANOSINE-5'-MONOPHOSPHATE / Hypoxanthine-guanine phosphoribosyltransferase
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.45 Å
AuthorsMoynie, L. / Giraud, M.F. / Breton, A. / Boissier, F. / Daignan-Fornier, B. / Dautant, A.
Citation
Journal: Protein Sci. / Year: 2012
Title: Functional Significance of Four Successive Glycine Residues in the Pyrophosphate Binding Loop of Fungal 6-Oxopurine Phosphoribosyltransferases.
Authors: Moynie, L. / Giraud, M.F. / Breton, A. / Boissier, F. / Daignan-Fornier, B. / Dautant, A.
#1: Journal: Genetics / Year: 2008
Title: Lethal Accumulation of Guanylic Nucleotides in Saccharomyces Cerevisiae Hpt1-Deregulated Mutants.
Authors: Breton, A. / Pinson, B. / Coulpier, F. / Giraud, M. / Dautant, A. / Daignan-Fornier, B.
#2: Journal: J.Mol.Biol. / Year: 1998
Title: Structures of Free and Complexed Forms of Escherichia Coli Xanthine-Guanine Phosphoribosyltransferase.
Authors: Vos, S. / Parry, R.J. / Burns, M.R. / De Jersey, J. / Martin, J.L.
#3: Journal: Biochemistry / Year: 1997
Title: Crystal Structure of Escherichia Coli Xanthine Phosphoribosyltransferase.
Authors: Vos, S. / De Jersey, J. / Martin, J.L.
History
DepositionSep 2, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Version format compliance
Revision 1.2Jan 30, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.3Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE
B: HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE
C: HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE
D: HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,20712
Polymers100,3704
Non-polymers1,8378
Water00
1
A: HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE
B: HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1046
Polymers50,1852
Non-polymers9194
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint-53.2 kcal/mol
Surface area19280 Å2
MethodPISA
2
C: HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE
D: HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1046
Polymers50,1852
Non-polymers9194
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-51.9 kcal/mol
Surface area19320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.077, 176.362, 91.109
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.5375, 0.4516, -0.7121), (0.4512, -0.5594, -0.6953), (-0.7124, -0.695, 0.097)15.052, 90.69, 67.318
2given(-0.1301, 0.988, 0.0834), (0.9868, 0.1372, -0.086), (-0.0964, 0.0711, -0.9928)-53.768, 48.004, 97.784
3given(0.4425, -0.6808, -0.5837), (-0.417, 0.42, -0.806), (0.7939, 0.6001, -0.098)39.955, 70.022, 37.059

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Components

#1: Protein
HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE / BYPASS OF REPRESSION BY ADENINE PROTEIN 6 / HGPRTASE / HGPRT


Mass: 25092.520 Da / Num. of mol.: 4 / Fragment: RESIDUES 2-221
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: Y1846 / Plasmid: PET-21 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q04178, hypoxanthine phosphoribosyltransferase
#2: Chemical
ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O8P
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4

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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: 4.73 Å3/Da / Density % sol: 74 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 1.6 M AMMONIUM SULPHATE, 4% PEG 400, 0.2 M NA-K TARTRATE, 50 MM NA CITRATE, 50 MM MES, PH 5.8, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 10, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.45→25 Å / Num. obs: 25753 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 120 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.5
Reflection shellResolution: 3.45→3.64 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 1.9 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JKY

2jky


Resolution: 3.45→32.94 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1302 5.1 %RANDOM
Rwork0.221 ---
obs0.221 25547 99.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 100.51 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 116.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20 Å20 Å2
2--26.9 Å20 Å2
3----27.38 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a0.86 Å0.88 Å
Refinement stepCycle: LAST / Resolution: 3.45→32.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6508 0 116 0 6624
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.511.5
X-RAY DIFFRACTIONc_mcangle_it2.772
X-RAY DIFFRACTIONc_scbond_it1.552
X-RAY DIFFRACTIONc_scangle_it2.722.5
LS refinement shellResolution: 3.45→3.67 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.35 210 5 %
Rwork0.347 4006 -
obs--99.9 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: ION.TOP

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