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- PDB-6jwq: Crystal structure of Plasmodium falciparum HPPK-DHPS wild type -

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Basic information

Entry
Database: PDB / ID: 6jwq
TitleCrystal structure of Plasmodium falciparum HPPK-DHPS wild type
Components7,8-dihydro-6-hydroxymethylpterin pyrophosphokinase-dihydropteroate synthase
KeywordsTRANSFERASE / TIM barrel / kinase
Function / homology
Function and homology information


2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase activity / dihydropteroate synthase activity / folic acid biosynthetic process / mitochondrial envelope / tetrahydrofolate biosynthetic process / kinase activity / phosphorylation / ATP binding / metal ion binding / cytosol
Similarity search - Function
Dihydropteroate synthase / 7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase, HPPK / 7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase HPPK superfamily / 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (HPPK) / Dihydropteroate synthase domain / Dihydropteroate synthase signature 2. / Pterin-binding domain / Pterin binding enzyme / Pterin-binding domain profile. / Dihydropteroate synthase-like
Similarity search - Domain/homology
ACETATE ION / ADENOSINE MONOPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / 7,8-dihydro-6-hydroxymethylpterin pyrophosphokinase-dihydropteroate synthase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
Model detailsCrystal structure of Plasmodium falciparum HPPK-DHPS apo form
AuthorsChitnumsub, P. / Jaruwat, A. / Yuthavong, Y.
Funding support Thailand, 1items
OrganizationGrant numberCountry
Synchrotron Light Research Institute Thailand
CitationJournal: Febs J. / Year: 2020
Title: The structure of Plasmodium falciparum hydroxymethyldihydropterin pyrophosphokinase-dihydropteroate synthase reveals the basis of sulfa resistance.
Authors: Chitnumsub, P. / Jaruwat, A. / Talawanich, Y. / Noytanom, K. / Liwnaree, B. / Poen, S. / Yuthavong, Y.
History
DepositionApr 21, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2020Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID / _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
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 7,8-dihydro-6-hydroxymethylpterin pyrophosphokinase-dihydropteroate synthase
B: 7,8-dihydro-6-hydroxymethylpterin pyrophosphokinase-dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,9769
Polymers171,9152
Non-polymers1,0617
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5380 Å2
ΔGint-58 kcal/mol
Surface area53810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.175, 137.224, 139.282
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 7,8-dihydro-6-hydroxymethylpterin pyrophosphokinase-dihydropteroate synthase / Dihydropteroate synthetase


Mass: 85957.492 Da / Num. of mol.: 2 / Fragment: HPPK
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: PPPK-DHPS / Plasmid: pET29a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta(DE3)pLysS / References: UniProt: Q25704

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Non-polymers , 6 types, 137 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Fragment: DHPS / Source method: obtained synthetically / Formula: Mg / References: dihydropteroate synthase
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.81 Å3/Da / Density % sol: 56.26 % / Mosaicity: 0.751 °
Crystal growTemperature: 298 K / Method: microbatch / pH: 9
Details: 0.1 M bicine buffer pH 9.0, 0.5-0.6 M Ca acetate and 20%w/v PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 11, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 65642 / % possible obs: 97.3 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.056 / Χ2: 1.065 / Net I/σ(I): 15.3 / Num. measured all: 307040
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.5-2.594.20.3855600.912183.1
2.59-2.694.30.34760760.963191.8
2.69-2.824.60.29965860.95198.6
2.82-2.964.90.22866950.9541100
2.96-3.154.90.15366770.9751100
3.15-3.394.90.09467101.0081100
3.39-3.734.90.05867231.0981100
3.73-4.274.80.03867681.1081100
4.27-5.384.70.03868321.7691100
5.38-304.60.01870150.848199.1

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0103refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
CRANKphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.917 / SU B: 9.819 / SU ML: 0.212 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.368 / ESU R Free: 0.272
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2574 6638 10.1 %RANDOM
Rwork0.2054 ---
obs0.2106 58935 97.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 120 Å2 / Biso mean: 63.656 Å2 / Biso min: 21.17 Å2
Baniso -1Baniso -2Baniso -3
1-6.6 Å20 Å2-0 Å2
2---3.53 Å20 Å2
3----3.07 Å2
Refinement stepCycle: final / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9410 0 65 130 9605
Biso mean--82.18 44.39 -
Num. residues----1138
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0199625
X-RAY DIFFRACTIONr_angle_refined_deg1.4961.97812988
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.65551124
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.08825.551472
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.399151879
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0391538
X-RAY DIFFRACTIONr_chiral_restr0.1040.21489
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027016
LS refinement shellResolution: 2.503→2.567 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 385 -
Rwork0.295 3599 -
all-3984 -
obs--81.27 %

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