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- PDB-1cjb: MALARIAL PURINE PHOSPHORIBOSYLTRANSFERASE -

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Basic information

Entry
Database: PDB / ID: 1cjb
TitleMALARIAL PURINE PHOSPHORIBOSYLTRANSFERASE
ComponentsPROTEIN (HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE)
KeywordsTRANSFERASE / MALARIA / PURINE SALVAGE / PHOSPHORIBOSYLTRANSFERASE / TRANSITION STATE INHIBITOR
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
Chem-IRP / PYROPHOSPHATE 2- / Hypoxanthine-guanine-xanthine phosphoribosyltransferase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsShi, W. / Li, C.M. / Tyler, P.C. / Furneaux, R.H. / Cahill, S.M. / Girvin, M.E. / Grubmeyer, C. / Schramm, V.L. / Almo, S.C.
CitationJournal: Biochemistry / Year: 1999
Title: The 2.0 A structure of malarial purine phosphoribosyltransferase in complex with a transition-state analogue inhibitor.
Authors: Shi, W. / Li, C.M. / Tyler, P.C. / Furneaux, R.H. / Cahill, S.M. / Girvin, M.E. / Grubmeyer, C. / Schramm, V.L. / Almo, S.C.
History
DepositionApr 8, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Aug 18, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 11, 2019Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.4Aug 9, 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_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.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_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: PROTEIN (HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE)
B: PROTEIN (HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE)
C: PROTEIN (HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE)
D: PROTEIN (HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,82920
Polymers105,5464
Non-polymers2,28316
Water7,332407
1
A: PROTEIN (HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE)
B: PROTEIN (HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE)
hetero molecules

A: PROTEIN (HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE)
B: PROTEIN (HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,82920
Polymers105,5464
Non-polymers2,28316
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
MethodPISA
2
C: PROTEIN (HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE)
D: PROTEIN (HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE)
hetero molecules

C: PROTEIN (HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE)
D: PROTEIN (HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,82920
Polymers105,5464
Non-polymers2,28316
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_755-x+2,y,-z+1/21
MethodPISA
Unit cell
Length a, b, c (Å)105.490, 110.390, 173.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.99991, -0.01289, 0.00457), (0.00039, 0.30677, 0.95178), (-0.01367, 0.9517, -0.30674)94.15427, -44.42832, 61.70115
2given(0.35214, 0.548, -0.75874), (-0.00985, 0.8128, 0.58246), (0.93589, -0.19763, 0.29162)124.64395, -34.62596, 71.9466
3given(0.33369, -0.54476, 0.76934), (-0.00443, 0.8152, 0.57916), (-0.94267, -0.19667, 0.26961)53.3175, -44.92856, 75.24376

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Components

#1: Protein
PROTEIN (HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE)


Mass: 26386.457 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Production host: Escherichia coli (E. coli)
References: UniProt: P20035, hypoxanthine phosphoribosyltransferase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-IRP / (1S)-1(9-DEAZAHYPOXANTHIN-9YL)1,4-DIDEOXY-1,4-IMINO-D-RIBITOL-5-PHOSPHATE


Mass: 346.233 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H15N4O7P
#4: Chemical
ChemComp-POP / PYROPHOSPHATE 2- / Pyrophosphate


Mass: 175.959 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H2O7P2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 407 / 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: 2.2 Å3/Da / Density % sol: 43 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115-20 mg/mlprotein1drop
220 %PEG40001reservoir
3100 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.98
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 67609 / % possible obs: 99.1 % / Redundancy: 4.2 % / Rsym value: 0.048 / Net I/σ(I): 45
Reflection shellResolution: 2→2.07 Å / Mean I/σ(I) obs: 32 / Rsym value: 0.1 / % possible all: 98.4
Reflection
*PLUS
Num. measured all: 286410 / Rmerge(I) obs: 0.048
Reflection shell
*PLUS
Highest resolution: 2 Å / Rmerge(I) obs: 0.1

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.8refinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BZY

1bzy


Resolution: 2→20 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.239 3367 5 %RANDOM
Rwork0.196 ---
obs-67148 98 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-8.219 Å20 Å20 Å2
2--16.69 Å20 Å2
3---16.2 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7333 0 136 407 7876
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.291
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2→2.09 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.279 418 5 %
Rwork0.266 7721 -
obs--96.5 %
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.196
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.279 / % reflection Rfree: 5 % / Rfactor Rwork: 0.266

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