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- PDB-1qk5: TOXOPLASMA GONDII HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE ... -

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Basic information

Entry
Database: PDB / ID: 1qk5
TitleTOXOPLASMA GONDII HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE WITH XMP, PYROPHOSPHATE AND TWO MG2+ IONS
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
PYROPHOSPHATE 2- / XANTHOSINE-5'-MONOPHOSPHATE / Hypoxanthine-guanine-xanthine phosphoribosyltransferase
Similarity search - Component
Biological speciesTOXOPLASMA GONDII (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsHeroux, A. / White, E.L. / Ross, L.J. / Davis, R.L. / Borhani, D.W.
Citation
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.
#1: 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.
#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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,50310
Polymers53,3232
Non-polymers1,1808
Water3,279182
1
A: HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE
B: HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE
hetero molecules

A: HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE
B: HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,00520
Polymers106,6464
Non-polymers2,35916
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area11590 Å2
ΔGint-73.9 kcal/mol
Surface area38570 Å2
MethodPQS
Unit cell
Length a, b, c (Å)55.208, 112.255, 144.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.951065, 0.000778, -0.308991), (-0.001881, -0.999993, 0.003272), (-0.308986, 0.003693, 0.951059)
Vector: 65.0005, 51.2194, 10.2374)
DetailsTHE BIOMOLECULE CONSISTS OF A HOMO- TETRAMERIC COMPLEXOF BIOPOLYMERSSUBUNITS C AND D OF THE HGPRT HOMOTETRAMER ARE GENERATEDBY ROTATION OF SUBUNITS A AND B ABOUT THECRYSTALLOGRAPHIC 2- FOLD AXIS PARALLEL TO B.

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Components

#1: Protein HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE / HGPRTASE


Mass: 26661.492 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TOXOPLASMA GONDII (eukaryote) / Strain: RH / Plasmid: PETC1-D150A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q26997, hypoxanthine phosphoribosyltransferase
#2: Chemical ChemComp-XMP / XANTHOSINE-5'-MONOPHOSPHATE / 5-MONOPHOSPHATE-9-BETA-D-RIBOFURANOSYL XANTHINE


Mass: 365.213 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N4O9P
#3: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2O7P2
#4: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 182 / 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: 43 %
Crystal growTemperature: 277 K / pH: 8.5
Details: 30% PEG 4000, 100 MM TRIS.CL (PH 8.5), 200 MM LI2SO4, 0.25 % BETA-OCTYLGLUCOPYRANOSIDE. THE CRYSTAL WAS GROWN IN THE PRESENCE OF 1 MM XANTHINE, 1 MM PRPP AND 10 MM MGCL2 AT 277 K.
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Details: drop consists of equal volume of protein and reservoir solutions
PH range low: 6 / PH range high: 5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110-20 mg/mlprotein1drop
21 mMIMP1drop
315-20 %PEG80001reservoir
4100 mMpotassium phosphate1reservoir
50.25 %octyl-beta-D-glucopyranoside1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1
DetectorType: PRINCETON SCIENTIFIC INSTRUMENTS 2K CCD / Detector: CCD / Date: Feb 15, 1998 / Details: PT-COATED MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.6→13 Å / Num. obs: 58200 / % possible obs: 98 % / Redundancy: 4.2 % / Biso Wilson estimate: 24.14 Å2 / Rsym value: 0.076 / Net I/σ(I): 10.3
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.373 / % possible all: 93.9
Reflection
*PLUS
Num. measured all: 245248 / Rmerge(I) obs: 0.076
Reflection shell
*PLUS
% possible obs: 93.9 % / Rmerge(I) obs: 0.373

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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: 1.6→13 Å / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.11647 / ESU R Free: 0.11121
Details: NO RESTRAINTS WERE IMPOSED ON THE ATOMS OF THE PYROPHOSPHATE GROUPS OR MAGNESIUM CATIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26099 2953 5 %RANDOM
Rwork0.23351 ---
obs-55139 98 %-
Displacement parametersBiso mean: 25.06 Å2
Refinement stepCycle: LAST / Resolution: 1.6→13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3472 0 70 182 3724
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0150.02
X-RAY DIFFRACTIONp_angle_d0.040.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0380.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.7092
X-RAY DIFFRACTIONp_mcangle_it2.4663
X-RAY DIFFRACTIONp_scbond_it2.2822
X-RAY DIFFRACTIONp_scangle_it3.533
X-RAY DIFFRACTIONp_plane_restr0.0120.02
X-RAY DIFFRACTIONp_chiral_restr0.1470.15
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
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.234
Solvent computation
*PLUS
Displacement parameters
*PLUS

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