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- PDB-5dkt: N-terminal His tagged apPOL exonuclease mutant -

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Basic information

Entry
Database: PDB / ID: 5dkt
TitleN-terminal His tagged apPOL exonuclease mutant
ComponentsPrex DNA polymerase
KeywordsTRANSFERASE / DNA 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-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
Plastid replication-repair enzyme
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsMilton, M.E. / Honzatko, R.B. / Choe, J.Y. / Nelson, S.W.
Funding support United States, 1items
OrganizationGrant numberCountry
Iowa State University College of Liberal Arts and Sciences United States
Citation
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.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2015
Title: Crystallization and preliminary X-ray analysis of the Plasmodium falciparum apicoplast DNA polymerase.
Authors: Milton, M.E. / Choe, J.Y. / Honzatko, R.B. / Nelson, S.W.
History
DepositionSep 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2016Group: Database references
Revision 1.2Oct 19, 2016Group: Database references
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Prex DNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,06211
Polymers76,1741
Non-polymers88810
Water1,13563
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Prex DNA polymerase
hetero molecules

A: Prex DNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,12422
Polymers152,3492
Non-polymers1,77520
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+5/61
Buried area5320 Å2
ΔGint-260 kcal/mol
Surface area56710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.775, 141.775, 148.759
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Prex DNA polymerase / Pfprex


Mass: 76174.250 Da / Num. of mol.: 1 / Fragment: UNP residues 1389-2016 / Mutation: D82N, E84Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: isolate 3D7 / Gene: POM1, PF14_0112 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 Gen-X / References: UniProt: Q8ILY1, DNA-directed DNA polymerase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.83 Å3/Da / Density % sol: 56.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium sulfate, 0.1 M MES monohydrate pH 6.5, 30%(w/v) PEG monomethyl ether 5000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 19706 / % possible obs: 97.8 % / Observed criterion σ(I): -1 / Redundancy: 4.2 % / Biso Wilson estimate: 47.25 Å2 / Rmerge(I) obs: 0.345 / Rpim(I) all: 0.195 / Rrim(I) all: 0.339 / Χ2: 1.07 / Net I/av σ(I): 3.373 / Net I/σ(I): 2.5 / Num. measured all: 82305
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Num. unique allCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
2.9-33.418810.0180.6680.72696.4
3-3.123.719130.1040.570.71697.30.991
3.12-3.273.919430.1820.4950.73998.10.878
3.27-3.44419290.2480.4110.83798.20.7450.855
3.44-3.65419380.4520.3490.86397.90.6330.727
3.65-3.944.219770.6580.2591.01398.30.4920.559
3.94-4.334.419610.8370.191.0998.30.3650.413
4.33-4.964.520020.9230.1371.24298.60.2680.302
4.96-6.244.620260.9190.1371.14498.20.2690.304
6.24-504.821360.990.0551.84796.70.1120.125

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
MR-Rosettaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2KFN

2kfn


Resolution: 2.9→47.346 Å / SU ML: 0.59 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2995 1970 10 %
Rwork0.2647 17724 -
obs0.2682 19694 97.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 206.99 Å2 / Biso mean: 53.5513 Å2 / Biso min: 0.38 Å2
Refinement stepCycle: final / Resolution: 2.9→47.346 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4795 0 46 63 4904
Biso mean--38.14 19.99 -
Num. residues----577
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034920
X-RAY DIFFRACTIONf_angle_d0.5496633
X-RAY DIFFRACTIONf_chiral_restr0.025736
X-RAY DIFFRACTIONf_plane_restr0.003838
X-RAY DIFFRACTIONf_dihedral_angle_d9.6171869
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8965-2.96890.40791260.38851143126990
2.9689-3.04920.42081360.37651209134596
3.0492-3.13890.41821370.36641232136997
3.1389-3.24020.35081390.34731258139798
3.2402-3.35590.37981380.33741241137998
3.3559-3.49030.3881400.31751259139999
3.4903-3.64910.32841400.29051262140298
3.6491-3.84140.2991400.27311262140298
3.8414-4.08190.28881410.25751267140899
4.0819-4.39690.26741420.21471275141798
4.3969-4.8390.25251430.20791292143599
4.839-5.53820.28561450.2121307145299
5.5382-6.9740.29291470.24871313146098
6.974-47.35270.19421560.20081404156097

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