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- PDB-9bps: Plasmodium falciparum apicoplast DNA polymerase mutant - K417M -

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Basic information

Entry
Database: PDB / ID: 9bps
TitlePlasmodium falciparum apicoplast DNA polymerase mutant - K417M
ComponentsPlastid replication-repair enzyme
KeywordsREPLICATION / DNA polymerase / apicoplast / A-family polymerase
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 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 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsUng, A.R. / Honzatko, R.B. / Nelson, S.W.
Funding support United States, 1items
OrganizationGrant numberCountry
Other government United States
CitationJournal: To Be Published
Title: Investigation of the structure and mechanism of the apicoplast DNA polymerase from Plasmodium falciparum
Authors: Ung, A.R. / Honzatko, R.B. / Nelson, S.W.
History
DepositionMay 8, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)148,51611
Polymers148,0102
Non-polymers5069
Water2,378132
1
A: Plastid replication-repair enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,2055
Polymers74,0051
Non-polymers2004
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Plastid replication-repair enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3116
Polymers74,0051
Non-polymers3065
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)144.931, 144.931, 166.383
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

#1: Protein Plastid replication-repair enzyme


Mass: 74004.906 Da / Num. of mol.: 2 / Mutation: K417M, D82N, E84Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: PF3D7_1411400 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8ILY1, DNA-directed DNA polymerase
#2: Chemical ChemComp-NA / SODIUM ION


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


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Equal parts protein and precipitant solutions. Protein solution: 18 mg/ml protein, 20 mM Tris, pH 8.0, 500 mM NaCl. Precipitant solution: PEG-1000 30% (v/v), 100 sodium citrate tribasic ...Details: Equal parts protein and precipitant solutions. Protein solution: 18 mg/ml protein, 20 mM Tris, pH 8.0, 500 mM NaCl. Precipitant solution: PEG-1000 30% (v/v), 100 sodium citrate tribasic dihydrate, pH 5.5, 500 mM NaCl
PH range: 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 7, 2022
Details: Cryogenically-cooled single crystal Si(220) side bounce monochromator. Optional Si(311) to achive 13.474 keV.
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 48658 / % possible obs: 100 % / Redundancy: 11.3 % / Biso Wilson estimate: 78.62 Å2 / CC1/2: 0.977 / CC star: 0.994 / Χ2: 0.889 / Net I/σ(I): 14.5
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 9.9 % / Num. unique obs: 2415 / CC1/2: 0.587 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIX1.19.2_4158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→47.44 Å / SU ML: 0.4219 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.1327
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2531 1984 4.11 %
Rwork0.2307 46238 -
obs0.2316 48222 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 86.8 Å2
Refinement stepCycle: LAST / Resolution: 2.8→47.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9522 0 27 132 9681
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059740
X-RAY DIFFRACTIONf_angle_d0.720313114
X-RAY DIFFRACTIONf_chiral_restr0.04811464
X-RAY DIFFRACTIONf_plane_restr0.00441668
X-RAY DIFFRACTIONf_dihedral_angle_d14.30393736
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.870.34011430.32913310X-RAY DIFFRACTION99.8
2.87-2.950.38031480.30223331X-RAY DIFFRACTION99.77
2.95-3.040.30671460.30013273X-RAY DIFFRACTION99.82
3.04-3.130.37031380.32973332X-RAY DIFFRACTION99.83
3.13-3.250.32981450.2953318X-RAY DIFFRACTION99.83
3.25-3.380.28871410.2723303X-RAY DIFFRACTION99.91
3.38-3.530.28441370.25483329X-RAY DIFFRACTION99.91
3.53-3.720.31761470.25923314X-RAY DIFFRACTION99.88
3.72-3.950.24391470.22513316X-RAY DIFFRACTION99.83
3.95-4.250.23591420.1983330X-RAY DIFFRACTION99.71
4.25-4.680.21161370.19553327X-RAY DIFFRACTION99.68
4.68-5.360.18661430.19273308X-RAY DIFFRACTION99.28
5.36-6.750.2371300.22643202X-RAY DIFFRACTION95.88
6.75-47.440.23281400.21393245X-RAY DIFFRACTION95.62

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