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

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Basic information

Entry
Database: PDB / ID: 3ozg
TitleCrystal Structure of Plasmodium falciparum Hypoxanthine-Guanine-Xanthine Phosphoribosyltransferase in complex with S-SerMe-ImmH phosphonate
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 / 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- / Chem-SSI / Hypoxanthine-guanine-xanthine phosphoribosyltransferase
Similarity search - Component
Biological speciesPlasmodium falciparum FCR-3/Gambia (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.993 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 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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)115,70916
Polymers113,6434
Non-polymers2,06612
Water3,801211
1
A: Hypoxanthine-guanine-xanthine phosphoribosyltransferase
B: Hypoxanthine-guanine-xanthine phosphoribosyltransferase
hetero molecules

A: Hypoxanthine-guanine-xanthine phosphoribosyltransferase
B: Hypoxanthine-guanine-xanthine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,70916
Polymers113,6434
Non-polymers2,06612
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area11440 Å2
ΔGint-92 kcal/mol
Surface area34670 Å2
MethodPISA
2
C: Hypoxanthine-guanine-xanthine phosphoribosyltransferase
D: Hypoxanthine-guanine-xanthine phosphoribosyltransferase
hetero molecules

C: Hypoxanthine-guanine-xanthine phosphoribosyltransferase
D: Hypoxanthine-guanine-xanthine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,70916
Polymers113,6434
Non-polymers2,06612
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_755-x+2,y,-z+1/21
Buried area11560 Å2
ΔGint-90 kcal/mol
Surface area34660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.095, 110.628, 173.336
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#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
#2: Chemical
ChemComp-SSI / [(3S)-4-hydroxy-3-{[(4-oxo-4,5-dihydro-3H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]amino}butyl]phosphonic acid / S-SerMe-ImmH phosphonate


Mass: 316.250 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H17N4O5P
#3: Chemical
ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 4 / 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.: 211 / 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: 2.22 Å3/Da / Density % sol: 44.51 %
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: 1.993→20 Å / Num. obs: 67657 / % possible obs: 98.5 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.149 / Net I/σ(I): 5.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.993-2.075.60.707188.7
2.07-2.155.90.61196
2.15-2.256.50.535199.9
2.25-2.377.30.4771100
2.37-2.527.80.4291100
2.52-2.7180.3141100
2.71-2.9980.2171100
2.99-3.427.90.1371100
3.42-4.37.70.0911100
4.3-207.70.0651100

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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
Starting model: PDB ENTRY 1CBJ

1cbj


Resolution: 1.993→19.98 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.913 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.718 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.217 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26418 3417 5.1 %RANDOM
Rwork0.21917 ---
obs0.22149 63967 97.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.718 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2---0.16 Å20 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.993→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7354 0 124 211 7689
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0227699
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5031.9810431
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1715927
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.71724.435345
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.985151349
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0611524
X-RAY DIFFRACTIONr_chiral_restr0.1020.21137
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215720
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5751.54577
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.09827448
X-RAY DIFFRACTIONr_scbond_it1.84133122
X-RAY DIFFRACTIONr_scangle_it2.8654.52974
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.993→2.044 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 202 -
Rwork0.307 3859 -
obs--81.27 %

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