9BPS | pdb_00009bps

Plasmodium falciparum apicoplast DNA polymerase mutant - K417M

PDB DOI: https://doi.org/10.2210/pdb9BPS/pdb

Classification: REPLICATION
Organism(s): Plasmodium falciparum 3D7
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2024-05-08 Released: 2025-05-14
Deposition Author(s): Ung, A.R., Honzatko, R.B., Nelson, S.W.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.253 (Depositor), 0.253 (DCC)
R-Value Work:
0.231 (Depositor), 0.228 (DCC)
R-Value Observed:
0.232 (Depositor)

Starting Model: experimental
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This is version 1.0 of the entry. See complete history.

Literature

Investigation of the structure and mechanism of the apicoplast DNA polymerase from Plasmodium falciparum

Ung, A.R., Honzatko, R.B., Nelson, S.W.

To be published.

Macromolecule Content

Total Structure Weight: 148.52 kDa
Atom Count: 9,710
Modeled Residue Count: 1,146
Deposited Residue Count: 1,256
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Plastid replication-repair enzyme	A, B	628	Plasmodium falciparum 3D7	Mutation(s): 3 Gene Names: PF3D7_1411400 EC: 2.7.7.7 (PDB Primary Data), 2.7.7.102 (UniProt), 5.6.2.3 (UniProt), 3.1.11 (UniProt)
UniProt
Find proteins for Q8ILY1 (Plasmodium falciparum (isolate 3D7)) Explore Q8ILY1 Go to UniProtKB: Q8ILY1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8ILY1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain G [auth B] SDF format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain G [auth B] MOL2 format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain G [auth B] mmCIF format, chain F [auth A]	F [auth A], G [auth B], K [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth B] Focus chain K [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth B] Focus chain K [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], I [auth B], J [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain C [auth A] MOL2 format, chain H [auth B] MOL2 format, chain C [auth A] mmCIF format, chain H [auth B] mmCIF format, chain C [auth A]	C [auth A], H [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.253 (Depositor), 0.253 (DCC)
R-Value Work: 0.231 (Depositor), 0.228 (DCC)
R-Value Observed: 0.232 (Depositor)

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.931	α = 90
b = 144.931	β = 90
c = 166.383	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-05-14

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government	United States	--

Revision History (Full details and data files)

Version 1.0: 2025-05-14
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.