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- PDB-6kcl: Crystal structure of Plasmodium falciparum HPPK-DHPS A437G/K540E ... -

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Basic information

Entry
Database: PDB / ID: 6kcl
TitleCrystal structure of Plasmodium falciparum HPPK-DHPS A437G/K540E with pterin and p-hydroxybenzoate
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-5'-TRIPHOSPHATE / PTERINE / P-HYDROXYBENZOIC ACID / 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: 2.7 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 Institute2008/08 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
DepositionJun 28, 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)173,93516
Polymers171,8872
Non-polymers2,04814
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7550 Å2
ΔGint-57 kcal/mol
Surface area49740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.323, 136.440, 137.699
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: 85943.398 Da / Num. of mol.: 2 / Fragment: HPPK-DHPS / Mutation: A437G, K540E
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, 206 molecules

#2: Chemical ChemComp-PE0 / PTERINE


Mass: 163.137 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5N5O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PHB / P-HYDROXYBENZOIC ACID


Mass: 138.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O3
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-MG / MAGNESIUM ION


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


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


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 2.71 Å3/Da / Density % sol: 54.68 % / Mosaicity: 0.396 °
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: Nov 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 51949 / % possible obs: 99.9 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.022 / Rrim(I) all: 0.054 / Χ2: 0.913 / Net I/σ(I): 16.5 / Num. measured all: 323274
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.86.20.36451190.9550.1580.3980.874100
2.8-2.916.20.26251380.9790.1140.2860.891100
2.91-3.046.20.18351240.990.0790.20.901100
3.04-3.26.30.12951680.9930.0550.1410.916100
3.2-3.46.40.08551400.9960.0360.0920.869100
3.4-3.666.30.06451650.9970.0270.071.04100
3.66-4.036.30.0551840.9980.0220.0551.03899.9
4.03-4.616.20.04252020.9980.0180.0461.27399.9
4.61-5.86.10.03352570.9980.0150.0360.93499.8
5.8-3060.015545210.0060.0160.39699.5

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JWR

6jwr


Resolution: 2.7→30 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.892 / SU B: 8.776 / SU ML: 0.188 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.571 / ESU R Free: 0.307
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2434 5154 10.1 %RANDOM
Rwork0.2018 ---
obs0.206 46023 98.36 %-
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: 50.471 Å2 / Biso min: 10.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2---0.47 Å20 Å2
3---0.54 Å2
Refinement stepCycle: final / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8903 0 130 192 9225
Biso mean--51.32 31.36 -
Num. residues----1078
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.029164
X-RAY DIFFRACTIONr_angle_refined_deg1.3221.98812366
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1651061
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.69825.618445
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.853151779
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2211535
X-RAY DIFFRACTIONr_chiral_restr0.0890.21426
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026654
LS refinement shellResolution: 2.701→2.771 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 340 -
Rwork0.231 2730 -
all-3070 -
obs--83.88 %

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