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

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Basic information

Entry
Database: PDB / ID: 7sxq
TitlePlasmodium falciparum apicoplast DNA polymerase (exo-minus) without affinity tag
ComponentsApicoplast DNA polymerase
KeywordsREPLICATION / TRANSFERASE / DNA polymerase / exonulease / apicoplast / Plasmodium falciparum
Function / homology
Function and homology information


apicoplast / mitochondrial DNA replication / DNA primase activity / DNA helicase activity / 3'-5' exonuclease activity / single-stranded DNA binding / 5'-3' DNA helicase activity / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / mitochondrion / 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 superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
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: 2.5 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
Citation
Journal: 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.
#1: Journal: J. Mol. Biol. / Year: 2016
Title: Crystal Structure of the Apicoplast DNA Polymerase from Plasmodium falciparum: The First Look at a Plastidic A-Family DNA Polymerase
Authors: Milton, M.E. / Choe, J.Y. / Honzatko, R.B. / Nelson, S.W.
History
DepositionNov 24, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 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: Apicoplast DNA polymerase
B: Apicoplast DNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,67315
Polymers147,9282
Non-polymers74513
Water7,837435
1
A: Apicoplast DNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3057
Polymers73,9641
Non-polymers3426
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Apicoplast DNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3688
Polymers73,9641
Non-polymers4047
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)143.999, 143.999, 165.006
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 Apicoplast DNA polymerase / Plastid replication-repair enzyme


Mass: 73963.852 Da / Num. of mol.: 2 / Mutation: D82N, E84Q, W512F
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 , 5 types, 448 molecules

#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 435 / 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: 3.34 Å3/Da / Density % sol: 63.16 % / Description: hexagonal bipyramidal
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: Equal parts of 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% ...Details: Equal parts of 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 mM 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: Jul 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 66691 / % possible obs: 100 % / Redundancy: 10.2 % / Biso Wilson estimate: 55.84 Å2 / CC1/2: 0.987 / Net I/σ(I): 17.8
Reflection shellResolution: 2.5→2.64 Å / Num. unique obs: 3368 / CC1/2: 0.568

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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: 2.5→19.97 Å / SU ML: 0.3075 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.1332
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2245 1996 3 %
Rwork0.2006 64508 -
obs0.2013 66504 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.09 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9540 0 40 435 10015
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00249817
X-RAY DIFFRACTIONf_angle_d0.444413212
X-RAY DIFFRACTIONf_chiral_restr0.04141472
X-RAY DIFFRACTIONf_plane_restr0.00291685
X-RAY DIFFRACTIONf_dihedral_angle_d10.22913771
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.570.33751440.29424597X-RAY DIFFRACTION99.94
2.57-2.640.29661380.25874590X-RAY DIFFRACTION100
2.64-2.710.26431470.2544607X-RAY DIFFRACTION99.98
2.71-2.80.28171370.25074596X-RAY DIFFRACTION100
2.8-2.90.25941420.24254589X-RAY DIFFRACTION100
2.9-3.020.26161380.2344584X-RAY DIFFRACTION100
3.02-3.150.26811400.22624617X-RAY DIFFRACTION100
3.15-3.320.29161460.22374610X-RAY DIFFRACTION100
3.32-3.530.22931440.20594605X-RAY DIFFRACTION99.98
3.53-3.80.21091420.19734588X-RAY DIFFRACTION100
3.8-4.170.20211410.17794593X-RAY DIFFRACTION100
4.17-4.770.18081460.16234639X-RAY DIFFRACTION100
4.77-5.980.2081460.18454621X-RAY DIFFRACTION100
5.98-19.970.20741450.18984672X-RAY DIFFRACTION99.94

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