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- PDB-1qk3: TOXOPLASMA GONDII HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE ... -

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Basic information

Entry
Database: PDB / ID: 1qk3
TitleTOXOPLASMA GONDII HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE GMP COMPLEX
ComponentsHYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE
KeywordsTRANSFERASE / GLYCOSYLTRANSFERASE / PURINE SALVAGE
Function / homology
Function and homology information


xanthine phosphoribosyltransferase / XMP salvage / xanthine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase / guanine phosphoribosyltransferase activity / GMP salvage / hypoxanthine phosphoribosyltransferase activity / IMP salvage / purine ribonucleoside salvage / nucleotide binding ...xanthine phosphoribosyltransferase / XMP salvage / xanthine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase / guanine phosphoribosyltransferase activity / GMP salvage / hypoxanthine phosphoribosyltransferase activity / IMP salvage / purine ribonucleoside salvage / nucleotide binding / metal ion binding / cytoplasm
Similarity search - Function
Hypoxanthine phosphoribosyl transferase / : / Purine/pyrimidine phosphoribosyl transferases signature. / 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-xanthine phosphoribosyltransferase
Similarity search - Component
Biological speciesTOXOPLASMA GONDII (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsHeroux, A. / White, E.L. / Ross, L.J. / Borhani, D.W.
Citation
Journal: Biochemistry / Year: 1999
Title: Crystal Structures of the Toxoplasma Gondii Hypoxanthine-Guanine Phosphoribosyltransferase Gmp and -Imp Complexes: Comparison of Purine Binding Interactions with the Xmp Complex
Authors: Heroux, A. / White, E.L. / Ross, L.J. / Borhani, D.W.
#1: Journal: Biochemistry / Year: 1999
Title: Crystal Structure of Toxoplasma Gondii Hypoxanthine-Guanine Phosphoribosyltransferase with Xmp, Pyrophosphate and Two Mg2+ Ions Bound: Insights Into the Catalytic Mechanism
Authors: Heroux, A. / White, E.L. / Ross, L.J. / Davis, R.L. / Borhani, D.W.
#2: Journal: Gene / Year: 1994
Title: Isolation and Sequencing of a Cdna Encoding the Hypoxanthine-Guanine Phosphoribosyltransferase from Toxoplasma Gondii
Authors: Vasanthakumar, G. / Van Ginkel, S. / Parish, G.
History
DepositionJul 9, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 1999Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)108,2758
Polymers106,8224
Non-polymers1,4534
Water11,620645
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11360 Å2
ΔGint-28.1 kcal/mol
Surface area46910 Å2
MethodPQS
Unit cell
Length a, b, c (Å)65.453, 90.842, 80.256
Angle α, β, γ (deg.)90.00, 92.53, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.998952, 0.03121, 0.033478), (0.031671, -0.056695, 0.997889), (0.033042, 0.997904, 0.055647)144.944, -18.2291, 12.689
2given(0.634533, -0.598264, 0.489333), (-0.586699, -0.784988, -0.198945), (0.503142, -0.160854, -0.849102)26.5256, 211.8541, 165.66859
3given(-0.626453, 0.562888, -0.539178), (0.55054, -0.170149, -0.817285), (-0.55178, -0.80883, -0.203302)131.9211, 139.1158, 232.24879
DetailsTHE BIOMOLECULE CONSISTS OF A HOMO- TETRAMERIC COMPLEXOF BIOPOLYMERS

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Components

#1: Protein
HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE / HGPRTASE


Mass: 26705.502 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TOXOPLASMA GONDII (eukaryote) / Strain: RH / Plasmid: PETC1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q26997, hypoxanthine phosphoribosyltransferase
#2: Chemical
ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O8P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 645 / 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: 2.09 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 277 K / pH: 5
Details: 15% PEG 8000, 100 MM KPO4 (PH 5-6), 0.25% BETA-OCTYLGLUCOPYRANOSIDE, 1 MM GMP, 277 K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / PH range low: 6 / PH range high: 5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115-20 %PEG80001reservoir
2100 mMpotassium phosphate1reservoir
30.25 %octyl brta-D-glucopyranoside1reservoir
410-20 mg/mlprotein1drop
51 mMGMP1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.908
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 15, 1996 / Details: RH MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.908 Å / Relative weight: 1
ReflectionResolution: 1.65→12.5 Å / Num. obs: 108535 / % possible obs: 96.4 % / Redundancy: 2.8 % / Biso Wilson estimate: 20.4 Å2 / Rsym value: 0.053 / Net I/σ(I): 9.4
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 2 % / Mean I/σ(I) obs: 1.7 / Rsym value: 0.459 / % possible all: 85.3
Reflection
*PLUS
Num. measured all: 302104 / Rmerge(I) obs: 0.053
Reflection shell
*PLUS
% possible obs: 85.3 % / Rmerge(I) obs: 0.459

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HMP, SUBUNIT A, WITHOUT LOOPS, WATERS, OR GMP

1hmp


Resolution: 1.65→12.5 Å / SU B: 1.27012 / SU ML: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.11491 / ESU R Free: 0.10941
Details: THE STRUCTURE WAS FIRST REFINED USING X-XPLOR. REFMAC AND ARP WERE USED TO FINISH THE REFINEMENT, USING THE X-PLOR-CALCULATED BULK SOLVENT CORRECTION.
RfactorNum. reflection% reflectionSelection details
Rfree0.231 5403 5 %RANDOM
Rwork0.202 ---
obs-103103 96.4 %-
Displacement parametersBiso mean: 22.2 Å2
Refinement stepCycle: LAST / Resolution: 1.65→12.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7197 0 96 645 7938
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.02
X-RAY DIFFRACTIONp_angle_d0.030.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0360.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.6642
X-RAY DIFFRACTIONp_mcangle_it2.5783
X-RAY DIFFRACTIONp_scbond_it1.9752
X-RAY DIFFRACTIONp_scangle_it3.1323
X-RAY DIFFRACTIONp_plane_restr0.01040.02
X-RAY DIFFRACTIONp_chiral_restr0.1280.15
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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