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- PDB-3phc: Crystal Structure of Plasmodium falciparum purine nucleoside phos... -

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Basic information

Entry
Database: PDB / ID: 3phc
TitleCrystal Structure of Plasmodium falciparum purine nucleoside phosphorylase in complex with DADMe-ImmG
ComponentsPurine nucleoside phosphorylase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / PNP / Immucillin / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


Pyrimidine salvage / Pyrimidine catabolism / S-methyl-5'-thioinosine phosphorylase / purine nucleotide catabolic process / uridine catabolic process / inosine catabolic process / S-methyl-5-thioadenosine phosphorylase activity / uridine phosphorylase activity / guanosine phosphorylase activity / purine-nucleoside phosphorylase activity ...Pyrimidine salvage / Pyrimidine catabolism / S-methyl-5'-thioinosine phosphorylase / purine nucleotide catabolic process / uridine catabolic process / inosine catabolic process / S-methyl-5-thioadenosine phosphorylase activity / uridine phosphorylase activity / guanosine phosphorylase activity / purine-nucleoside phosphorylase activity / purine-nucleoside phosphorylase / purine ribonucleoside salvage / cytosol
Similarity search - Function
Nucleoside phosphorylase domain / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-IM5 / : / PHOSPHATE ION / Purine nucleoside phosphorylase / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsHo, M. / Edwards, A.A. / Almo, S.C. / Schramm, V.L.
CitationJournal: To be Published
Title: Crystal Structure of Plasmodium falciparum purine nucleoside phosphorylase in complex with DADMe-ImmG
Authors: Ho, M. / Edwards, A.A. / Almo, S.C. / Schramm, V.L.
History
DepositionNov 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Feb 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_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_conn.ptnr2_label_seq_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: Purine nucleoside phosphorylase
B: Purine nucleoside phosphorylase
C: Purine nucleoside phosphorylase
D: Purine nucleoside phosphorylase
E: Purine nucleoside phosphorylase
F: Purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,94921
Polymers182,5866
Non-polymers2,36315
Water5,621312
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22640 Å2
ΔGint-117 kcal/mol
Surface area46360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.197, 77.371, 92.197
Angle α, β, γ (deg.)67.710, 73.620, 86.030
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Purine nucleoside phosphorylase


Mass: 30430.961 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: PNP / Plasmid: pTrcHis2 TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8T9Z7, UniProt: Q8I3X4*PLUS, purine-nucleoside phosphorylase
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-IM5 / 2-amino-7-{[(3R,4R)-3-hydroxy-4-(hydroxymethyl)pyrrolidin-1-yl]methyl}-3,5-dihydro-4H-pyrrolo[3,2-d]pyrimidin-4-one / DADMe-ImmG


Mass: 279.295 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C12H17N5O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 2.12 Å3/Da / Density % sol: 41.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 0.1M sodium formate, 10% PEG 3350, 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
DetectorDetector: CCD / Date: Dec 4, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 95778 / % possible obs: 94.2 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.059 / Χ2: 1.011 / Net I/σ(I): 11.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.073.10.15280481.009178.9
2.07-2.153.10.13887131.005186.1
2.15-2.253.10.12493881.028192.1
2.25-2.373.20.1197221.006195.7
2.37-2.523.20.09698551.023197.4
2.52-2.713.20.08299851.018197.7
2.71-2.993.20.06899681.019198.1
2.99-3.423.20.057100221.006198.5
3.42-4.33.20.046100050.95198.7
4.3-203.20.041100721.042199.1

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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
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.931 / Occupancy max: 1 / Occupancy min: 1 / SU B: 4.362 / SU ML: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2349 4781 5 %RANDOM
Rwork0.1977 ---
obs0.1995 95775 93.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 57.81 Å2 / Biso mean: 29.7476 Å2 / Biso min: 12.75 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å22.35 Å21.48 Å2
2--0.38 Å22.21 Å2
3----3.54 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11166 0 153 312 11631
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02211514
X-RAY DIFFRACTIONr_angle_refined_deg1.3171.98615594
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.05151452
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.92924.81474
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.274152004
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0611554
X-RAY DIFFRACTIONr_chiral_restr0.0880.21788
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218496
X-RAY DIFFRACTIONr_mcbond_it0.5591.57224
X-RAY DIFFRACTIONr_mcangle_it1.055211652
X-RAY DIFFRACTIONr_scbond_it1.67834290
X-RAY DIFFRACTIONr_scangle_it2.724.53942
LS refinement shellResolution: 2→2.046 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 275 -
Rwork0.25 5203 -
all-5478 -
obs--72.83 %

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