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- PDB-6jwz: Crystal structure of Plasmodium falciparum HPPK-DHPS S436F/A437G/... -

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Basic information

Entry
Database: PDB / ID: 6jwz
TitleCrystal structure of Plasmodium falciparum HPPK-DHPS S436F/A437G/A613S triple mutant with SDX-DHP
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 / mitochondrial envelope / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / kinase activity / ATP binding / metal ion binding
Similarity search - Function
7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase, HPPK / 7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase HPPK superfamily / 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (HPPK) / Dihydropteroate synthase / 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 / Chem-CKL / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / 7,8-dihydro-6-hydroxymethylpterin pyrophosphokinase-dihydropteroate synthase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
Model detailsCrystal structure of Plasmodium falciparum HPPK-DHPS wild type with Pteroate
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 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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)174,35816
Polymers172,0392
Non-polymers2,31814
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6300 Å2
ΔGint-80 kcal/mol
Surface area52850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.198, 136.826, 138.690
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: 86019.555 Da / Num. of mol.: 2 / Fragment: HPPK-DHPS / Mutation: S436F/A437G/A613S
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 , 8 types, 163 molecules

#2: Chemical ChemComp-CKL / 4-[(2-azanyl-4-oxidanylidene-7,8-dihydro-3~{H}-pteridin-6-yl)methylamino]-~{N}-(5,6-dimethoxypyrimidin-4-yl)benzenesulfonamide


Mass: 487.492 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H21N9O5S
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#7: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.76 Å3/Da / Density % sol: 55.48 % / Mosaicity: 1.254 °
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 29, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.95→30 Å / Num. obs: 40148 / % possible obs: 98.7 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.056 / Χ2: 0.941 / Net I/σ(I): 13.7 / Num. measured all: 178346
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.95-3.063.90.38338140.967195.9
3.06-3.1840.28139190.944197.6
3.18-3.324.10.18739730.966198.5
3.32-3.54.30.13939630.962199.4
3.5-3.724.50.09440460.979199.8
3.72-44.80.06740240.895199.8
4-4.44.80.04740610.838199.6
4.4-5.044.80.04240490.962199.3
5.04-6.344.70.04440861.046199
6.34-304.60.0342130.87197.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JWQ

6jwq


Resolution: 2.95→29.57 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.869 / SU B: 14.189 / SU ML: 0.273 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.437
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2549 3627 10 %RANDOM
Rwork0.1942 ---
obs0.2003 32706 89.32 %-
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: 49.834 Å2 / Biso min: 4.31 Å2
Baniso -1Baniso -2Baniso -3
1-1.02 Å20 Å20 Å2
2---0.23 Å20 Å2
3----0.78 Å2
Refinement stepCycle: final / Resolution: 2.95→29.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9206 0 150 149 9505
Biso mean--57.37 33.83 -
Num. residues----1115
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0129497
X-RAY DIFFRACTIONr_angle_refined_deg1.3041.65212808
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.69451100
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.08124.435496
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.172151848
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1981537
X-RAY DIFFRACTIONr_chiral_restr0.1050.21257
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026857
LS refinement shellResolution: 2.954→3.03 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 112 -
Rwork0.23 1119 -
all-1231 -
obs--42.13 %

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