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- PDB-6jwr: Crystal structure of Plasmodium falciparum HPPK-DHPS wild type wi... -

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Basic information

Entry
Database: PDB / ID: 6jwr
TitleCrystal structure of Plasmodium falciparum HPPK-DHPS wild type with Pteroate
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-PH2 / PTEROIC 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: 2.6 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 ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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
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

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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)173,99619
Polymers171,9152
Non-polymers2,08117
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8060 Å2
ΔGint-86 kcal/mol
Surface area50740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.726, 137.006, 138.409
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-DHPS
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) / Variant (production host): BL21 Rosetta(DE3)pLysS / References: UniProt: Q25704

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Non-polymers , 7 types, 202 molecules

#2: Chemical ChemComp-PT1 / PTEROIC ACID


Mass: 312.283 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H12N6O3
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


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


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-PH2 / 2-AMINO-6-HYDROXYMETHYL-7,8-DIHYDRO-3H-PTERIDIN-4-ONE


Mass: 195.179 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H9N5O2
#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.: 7 / Source method: obtained synthetically / Formula: C2H3O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.69 Å3/Da / Density % sol: 54.36 % / Mosaicity: 0.346 °
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: 2.6→30 Å / Num. obs: 57513 / % possible obs: 99.3 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.021 / Rrim(I) all: 0.052 / Χ2: 0.928 / Net I/σ(I): 17.5 / Num. measured all: 356489
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.696.10.46153870.9350.1980.5030.95794.3
2.69-2.86.10.37756850.9540.1630.4110.97699.5
2.8-2.936.20.25756880.980.1110.280.95799.9
2.93-3.086.20.1757460.9920.0740.1860.97299.9
3.08-3.286.30.10757390.9960.0460.1170.93699.9
3.28-3.536.30.06957770.9980.0290.0750.87299.9
3.53-3.886.30.04557600.9990.0190.0490.808100
3.88-4.446.20.04358380.9980.0180.0471.11100
4.44-5.596.10.03458440.9990.0150.0370.9499.9
5.59-3060.012604910.0050.0130.76299.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JWQ

6jwq


Resolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.889 / SU B: 8.785 / SU ML: 0.195 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.562 / ESU R Free: 0.313
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2542 5226 9.9 %RANDOM
Rwork0.2112 ---
obs0.2154 47686 91.49 %-
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: 52.044 Å2 / Biso min: 10.66 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å2-0 Å2
2---0.27 Å20 Å2
3---0.1 Å2
Refinement stepCycle: final / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9052 0 139 185 9376
Biso mean--44.55 33.35 -
Num. residues----1098
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0199334
X-RAY DIFFRACTIONr_bond_other_d0.0040.0212
X-RAY DIFFRACTIONr_angle_refined_deg1.521.98712603
X-RAY DIFFRACTIONr_angle_other_deg1.728326
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.60151081
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.96425.568449
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.228151782
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7961534
X-RAY DIFFRACTIONr_chiral_restr0.1060.21448
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026827
X-RAY DIFFRACTIONr_gen_planes_other0.0020.026
LS refinement shellResolution: 2.6→2.667 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 286 -
Rwork0.229 2316 -
all-2602 -
obs--62.14 %

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