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- PDB-7tux: Crystal Structure of Plasmodium falciparum Hypoxanthine-Guanine-X... -

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Basic information

Entry
Database: PDB / ID: 7tux
TitleCrystal Structure of Plasmodium falciparum Hypoxanthine-Guanine-Xanthine Phosphoribosyltransferase in complex with [(3S)-4-Hydroxy-3-[({2-amino-4-hydroxy-5H-pyrrolo[3,2-d]pyrimidin-7-yl}methyl)amino]butyl]phosphonic acid
ComponentsHypoxanthine-guanine-xanthine phosphoribosyltransferase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / inhibitors / drug design / transferase-inhibitor complex / Malaria / transition state analogs / transferase / Plasmodium falciparum / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


xanthine phosphoribosyltransferase / XMP salvage / xanthine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase / guanine salvage / hypoxanthine metabolic process / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / GMP salvage / IMP salvage ...xanthine phosphoribosyltransferase / XMP salvage / xanthine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase / guanine salvage / hypoxanthine metabolic process / guanine phosphoribosyltransferase activity / 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. / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain
Similarity search - Domain/homology
ACETIC ACID / PYROPHOSPHATE 2- / Chem-YBM / Hypoxanthine-guanine-xanthine phosphoribosyltransferase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsHarijan, R.K. / Minnow, Y.V.T. / Bonanno, J.B. / Almo, S.C. / Schramm, V.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI127807 United States
CitationJournal: Acs Chem.Biol. / Year: 2022
Title: Inhibition and Mechanism of Plasmodium falciparum Hypoxanthine-Guanine-Xanthine Phosphoribosyltransferase.
Authors: V T Minnow, Y. / Suthagar, K. / Clinch, K. / Ducati, R.G. / Ghosh, A. / Buckler, J.N. / Harijan, R.K. / Cahill, S.M. / Tyler, P.C. / Schramm, V.L.
History
DepositionFeb 3, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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)118,36458
Polymers113,6434
Non-polymers4,72154
Water13,890771
1
A: Hypoxanthine-guanine-xanthine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,56114
Polymers28,4111
Non-polymers1,15013
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Hypoxanthine-guanine-xanthine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,74717
Polymers28,4111
Non-polymers1,33616
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Hypoxanthine-guanine-xanthine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,68316
Polymers28,4111
Non-polymers1,27215
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Hypoxanthine-guanine-xanthine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,37311
Polymers28,4111
Non-polymers96210
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)105.437, 111.199, 173.652
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETAA1 - 22820 - 247
21METMETBB1 - 22820 - 247
12METMETAA1 - 22820 - 247
22METMETCC1 - 22820 - 247
13METMETAA1 - 22820 - 247
23METMETDD1 - 22820 - 247
14METMETBB1 - 22820 - 247
24METMETCC1 - 22820 - 247
15HISHISBB0 - 22819 - 247
25HISHISDD0 - 22819 - 247
16METMETCC1 - 22820 - 247
26METMETDD1 - 22820 - 247

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 28410.695 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: LACZ / Production host: Escherichia coli (E. coli)
References: UniProt: P20035, xanthine phosphoribosyltransferase, hypoxanthine phosphoribosyltransferase

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Non-polymers , 6 types, 825 molecules

#2: Chemical
ChemComp-YBM / [(3S)-3-{[(2-amino-4-hydroxy-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]amino}-4-hydroxybutyl]phosphonic acid


Mass: 331.265 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H18N5O5P / Feature type: SUBJECT OF INVESTIGATION
#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: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H4O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 771 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.3 Å3/Da / Density % sol: 45.08 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 200 mM Lithium Acetate, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Apr 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.62→173.65 Å / Num. obs: 128959 / % possible obs: 99.9 % / Redundancy: 7.4 % / CC1/2: 0.99 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.9
Reflection shellResolution: 1.62→1.65 Å / Redundancy: 6 % / Rmerge(I) obs: 1.07 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 6298 / CC1/2: 0.75 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OZF

3ozf


Resolution: 1.62→57.47 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.413 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1947 6509 5 %RANDOM
Rwork0.1696 ---
obs0.1708 122388 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 73.06 Å2 / Biso mean: 25.517 Å2 / Biso min: 14.91 Å2
Baniso -1Baniso -2Baniso -3
1-3.18 Å20 Å20 Å2
2---1.55 Å20 Å2
3----1.63 Å2
Refinement stepCycle: final / Resolution: 1.62→57.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7405 0 296 771 8472
Biso mean--33.9 37.36 -
Num. residues----922
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0138062
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177553
X-RAY DIFFRACTIONr_angle_refined_deg1.4061.66910877
X-RAY DIFFRACTIONr_angle_other_deg1.2781.59117566
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7635972
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.90223.522372
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.068151384
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0971524
X-RAY DIFFRACTIONr_chiral_restr0.0650.21000
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028831
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021657
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A75580.07
12B75580.07
21A75550.07
22C75550.07
31A76110.07
32D76110.07
41B75020.08
42C75020.08
51B75290.08
52D75290.08
61C75190.06
62D75190.06
LS refinement shellResolution: 1.62→1.662 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 484 -
Rwork0.3 8968 -
all-9452 -
obs--99.77 %

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