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- PDB-7sxl: Plasmodium falciparum apicoplast DNA polymerase (exo-minus) witho... -

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Basic information

Entry
Database: PDB / ID: 7sxl
TitlePlasmodium falciparum apicoplast DNA polymerase (exo-minus) without affinity tag
ComponentsPlastid replication-repair enzyme
KeywordsREPLICATION / Transferase / DNA polymerase / exonulease / apicoplast
Function / homology
Function and homology information


apicoplast / 3'-5' exonuclease activity / DNA helicase activity / DNA-templated DNA replication / single-stranded DNA binding / 5'-3' DNA helicase activity / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / ATP binding
Similarity search - Function
AAA domain / Twinkle-like protein / Archaeal primase DnaG/twinkle-like, TOPRIM domain / DNA helicase, DnaB-like, C-terminal / Superfamily 4 helicase domain profile. / 3'-5' exonuclease / 3'-5' exonuclease / 3'-5' exonuclease domain / DNA polymerase A / DNA polymerase family A ...AAA domain / Twinkle-like protein / Archaeal primase DnaG/twinkle-like, TOPRIM domain / DNA helicase, DnaB-like, C-terminal / Superfamily 4 helicase domain profile. / 3'-5' exonuclease / 3'-5' exonuclease / 3'-5' exonuclease domain / DNA polymerase A / DNA polymerase family A / DNA-directed DNA polymerase, family A, palm domain / DNA polymerase A domain / Toprim domain profile. / TOPRIM domain / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Plastid replication-repair enzyme
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsNieto, N. / Chheda, P. / Kerns, R. / Nelson, S. / Honzatko, R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM008365 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21AI127622 United States
CitationJournal: Eur.J.Med.Chem. / Year: 2022
Title: Promising antimalarials targeting apicoplast DNA polymerase from Plasmodium falciparum.
Authors: Chheda, P.R. / Nieto, N. / Kaur, S. / Beck, J.M. / Beck, J.R. / Honzatko, R. / Kerns, R.J. / Nelson, S.W.
History
DepositionNov 23, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Plastid replication-repair enzyme
B: Plastid replication-repair enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,28022
Polymers148,0062
Non-polymers1,27520
Water6,684371
1
A: Plastid replication-repair enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,74612
Polymers74,0031
Non-polymers74311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Plastid replication-repair enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,53410
Polymers74,0031
Non-polymers5319
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)145.369, 145.369, 164.944
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Plastid replication-repair enzyme


Mass: 74002.891 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / Gene: PF3D7_1411400
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q8ILY1, DNA-directed DNA polymerase

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Non-polymers , 6 types, 391 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 371 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.4 Å3/Da / Density % sol: 63.82 % / Description: Hexagonal bipyramidal
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: Equal parts protein and precipitant solutions. Protein solution: 20 mg/ml protein, 20 mM Tris, pH 8.0, 500 mM NaCl, 10% glycerol and 5 mM imidazole. Precipitant solution: PEG 1000 30% (v/v), ...Details: Equal parts protein and precipitant solutions. Protein solution: 20 mg/ml protein, 20 mM Tris, pH 8.0, 500 mM NaCl, 10% glycerol and 5 mM imidazole. Precipitant solution: PEG 1000 30% (v/v), 100 sodium citrate tribasic dihydrate, pH 5.5, 400 mM NaCl.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→19.91 Å / Num. obs: 54200 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 61.4 Å2 / CC1/2: 0.99 / Net I/σ(I): 0.8
Reflection shellResolution: 2.7→2.75 Å / Num. unique obs: 2312 / CC1/2: 0.539

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DKU

5dku


Resolution: 2.7→19.91 Å / SU ML: 0.3206 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.578
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2237 2005 3.71 %
Rwork0.1905 52058 -
obs0.1918 54063 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 72.97 Å2
Refinement stepCycle: LAST / Resolution: 2.7→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9538 0 72 371 9981
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00439826
X-RAY DIFFRACTIONf_angle_d0.55213218
X-RAY DIFFRACTIONf_chiral_restr0.0421470
X-RAY DIFFRACTIONf_plane_restr0.00361682
X-RAY DIFFRACTIONf_dihedral_angle_d10.283766
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.770.31311410.26693652X-RAY DIFFRACTION98.72
2.77-2.840.30681470.25523714X-RAY DIFFRACTION100
2.84-2.920.30541420.2593725X-RAY DIFFRACTION100
2.92-3.020.31721450.24393700X-RAY DIFFRACTION100
3.02-3.130.27381410.22843712X-RAY DIFFRACTION99.97
3.13-3.250.26681410.23333710X-RAY DIFFRACTION100
3.25-3.40.26611460.21223721X-RAY DIFFRACTION100
3.4-3.580.23781370.20123703X-RAY DIFFRACTION100
3.58-3.80.24891440.18733739X-RAY DIFFRACTION100
3.8-4.090.23641380.17383713X-RAY DIFFRACTION100
4.09-4.50.1811460.15283730X-RAY DIFFRACTION100
4.5-5.140.17341450.15493725X-RAY DIFFRACTION100
5.14-6.430.21531400.19163749X-RAY DIFFRACTION100
6.44-19.910.17771520.17723765X-RAY DIFFRACTION99.82

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