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- PDB-1qk4: TOXOPLASMA GONDII HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE ... -

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Basic information

Entry
Database: PDB / ID: 1qk4
TitleTOXOPLASMA GONDII HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE IMP 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 / guanine salvage / hypoxanthine metabolic process / hypoxanthine phosphoribosyltransferase activity / GMP salvage / IMP salvage ...xanthine phosphoribosyltransferase / XMP salvage / xanthine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase / guanine phosphoribosyltransferase activity / guanine salvage / hypoxanthine metabolic process / hypoxanthine phosphoribosyltransferase activity / GMP salvage / IMP salvage / purine ribonucleoside salvage / nucleotide binding / magnesium ion binding / cytosol
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
INOSINIC ACID / Hypoxanthine-guanine-xanthine phosphoribosyltransferase
Similarity search - Component
Biological speciesTOXOPLASMA GONDII (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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)108,2158
Polymers106,8224
Non-polymers1,3934
Water8,737485
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12100 Å2
ΔGint-30.8 kcal/mol
Surface area41340 Å2
MethodPQS
Unit cell
Length a, b, c (Å)84.537, 102.445, 108.825
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.089903, 0.514649, 0.852674), (0.525761, -0.702602, 0.479505), (0.845868, 0.491412, -0.207416)-4.3384, 0.3932, 4.5032
2given(0.078719, -0.354548, -0.931718), (-0.350188, -0.884891, 0.307142), (-0.933366, 0.302099, -0.193817)3.7862, 1.1351, 4.0957
3given(-0.982847, -0.161874, 0.088365), (-0.167769, 0.585808, -0.792895), (0.076584, -0.794119, -0.602918)-0.6762, 3.7328, 7.4582
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-IMP / INOSINIC ACID


Mass: 348.206 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H13N4O8P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 485 / 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: 2.21 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 277 K / pH: 8.5
Details: 30% PEG 4000, 100 MM TRIS (PH 8.5), 200 MM LI2SO4, 0.25 % BETA-OCTYLGLUCOPYRANOSIDE 1 MM IMP, 277 K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110-20 mg/mlprotein1drop
21 mMIMP1drop
330 %PEG40001reservoir
4100 mMTris-HCl1reservoir
5200 mM1reservoirLi2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 1997 / Details: PT-COATED MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.9→12.5 Å / Num. obs: 74791 / % possible obs: 99.6 % / Redundancy: 4.1 % / Biso Wilson estimate: 19.863 Å2 / Rsym value: 0.076 / Net I/σ(I): 10.7
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 4 % / Mean I/σ(I) obs: 3.5 / Rsym value: 0.383 / % possible all: 100
Reflection
*PLUS
Num. measured all: 305699 / Rmerge(I) obs: 0.076
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.383

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QK3, SUBUNIT A, WITHOUT LOOPS, WATERS, OR GMP

1qk3


Resolution: 1.9→12.5 Å / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.16026 / ESU R Free: 0.15181
Details: X-PLOR WAS USED IN THE EARLY STAGES OF REFINEMENT. REFMAC AND ARP WERE USED TO FINISH THE REFINEMENT, USING THE X-PLOR-CALCULATED BULK SOLVENT CORRECTION.
RfactorNum. reflection% reflectionSelection details
Rfree0.238 3778 5 %RANDOM
Rwork0.189 ---
obs-70933 99.6 %-
Displacement parametersBiso mean: 22.81 Å2
Refinement stepCycle: LAST / Resolution: 1.9→12.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7079 0 92 485 7656
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.02
X-RAY DIFFRACTIONp_angle_d0.0330.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0380.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.92
X-RAY DIFFRACTIONp_mcangle_it2.7773
X-RAY DIFFRACTIONp_scbond_it2.2662
X-RAY DIFFRACTIONp_scangle_it3.563
X-RAY DIFFRACTIONp_plane_restr0.01180.02
X-RAY DIFFRACTIONp_chiral_restr0.1420.15
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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