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- PDB-3ozf: Crystal Structure of Plasmodium falciparum Hypoxanthine-Guanine-X... -

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Basic information

Entry
Database: PDB / ID: 3ozf
TitleCrystal Structure of Plasmodium falciparum Hypoxanthine-Guanine-Xanthine Phosphoribosyltransferase in complex with hypoxanthine
ComponentsHypoxanthine-guanine-xanthine phosphoribosyltransferase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / hypoxanthine / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


xanthine phosphoribosyltransferase / XMP salvage / xanthine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase / GMP salvage / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / IMP salvage / purine ribonucleoside salvage / nucleotide binding ...xanthine phosphoribosyltransferase / XMP salvage / xanthine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase / GMP salvage / guanine phosphoribosyltransferase activity / 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
HYPOXANTHINE / PHOSPHATE ION / PYROPHOSPHATE 2- / Hypoxanthine-guanine-xanthine phosphoribosyltransferase
Similarity search - Component
Biological speciesPlasmodium falciparum FCR-3/Gambia (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.944 Å
AuthorsHo, M. / Hazleton, K.Z. / Almo, S.C. / Schramm, V.L.
CitationJournal: Chem.Biol. / Year: 2012
Title: Acyclic Immucillin Phosphonates: Second-Generation Inhibitors of Plasmodium falciparum Hypoxanthine- Guanine-Xanthine Phosphoribosyltransferase.
Authors: Hazleton, K.Z. / Ho, M.C. / Cassera, M.B. / Clinch, K. / Crump, D.R. / Rosario, I. / Merino, E.F. / Almo, S.C. / Tyler, P.C. / Schramm, V.L.
History
DepositionSep 24, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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_asym_id / _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_asym_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_ref_seq_dif.details / _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-xanthine phosphoribosyltransferase
B: Hypoxanthine-guanine-xanthine phosphoribosyltransferase
C: Hypoxanthine-guanine-xanthine phosphoribosyltransferase
D: Hypoxanthine-guanine-xanthine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,41722
Polymers113,6434
Non-polymers1,77418
Water7,368409
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13850 Å2
ΔGint-142 kcal/mol
Surface area35700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.035, 88.907, 80.371
Angle α, β, γ (deg.)90.000, 117.060, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Hypoxanthine-guanine-xanthine phosphoribosyltransferase / HGXPRTase / HGXPRT / HGPRT


Mass: 28410.695 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum FCR-3/Gambia (eukaryote)
Gene: LACZ / Plasmid: pDEST14 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P20035, Transferases; Glycosyltransferases; Pentosyltransferases

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Non-polymers , 5 types, 427 molecules

#2: Chemical
ChemComp-HPA / HYPOXANTHINE / Hypoxanthine


Mass: 136.111 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H4N4O
#3: Chemical
ChemComp-POP / PYROPHOSPHATE 2- / Pyrophosphate


Mass: 175.959 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H2O7P2
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 409 / 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: 2.1 Å3/Da / Density % sol: 41.45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 200mM sodium citrate, 20% PEG3350, pH 7.4, vapor diffusion, sitting drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 8, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 1.944→50 Å / Num. obs: 68909 / % possible obs: 99.9 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.093 / Χ2: 1.039 / Net I/σ(I): 10.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.944-2.024.50.41368511.051199.9
2.02-2.14.90.35768441.074199.9
2.1-2.250.25968851.0511100
2.2-2.314.90.23568561.021199.9
2.31-2.4650.16868791.0261100
2.46-2.6550.12468771.0321100
2.65-2.9150.168971.0151100
2.91-3.3350.07569051.071100
3.33-4.24.80.0669011.097199.8
4.2-504.80.04670140.952199.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.944→35.78 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.921 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.721 / SU ML: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.183 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2367 3498 5.1 %RANDOM
Rwork0.1893 ---
obs0.1917 68874 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 49.16 Å2 / Biso mean: 20.9429 Å2 / Biso min: 9.79 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20.08 Å2
2---0.13 Å20 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.944→35.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7429 0 102 409 7940
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0227723
X-RAY DIFFRACTIONr_angle_refined_deg1.5281.97410448
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0445925
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.23724.269349
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.038151352
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5891527
X-RAY DIFFRACTIONr_chiral_restr0.1160.21132
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215751
X-RAY DIFFRACTIONr_mcbond_it0.7451.54608
X-RAY DIFFRACTIONr_mcangle_it1.47927487
X-RAY DIFFRACTIONr_scbond_it2.47833115
X-RAY DIFFRACTIONr_scangle_it3.9334.52958
LS refinement shellResolution: 1.944→1.994 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 235 -
Rwork0.215 4592 -
all-4827 -
obs--95.41 %

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