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- PDB-5dku: C-terminal His tagged apPOL exonuclease mutant -

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Basic information

Entry
Database: PDB / ID: 5dku
TitleC-terminal His tagged apPOL exonuclease mutant
ComponentsPrex DNA polymerase
KeywordsTRANSFERASE / DNA polymerase
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
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
CitationJournal: 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
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.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Prex DNA polymerase
B: Prex DNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,9204
Polymers149,8722
Non-polymers492
Water1,67593
1
A: Prex DNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,9602
Polymers74,9361
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Prex DNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,9602
Polymers74,9361
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)146.382, 146.382, 165.671
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Prex DNA polymerase / Pfprex


Mass: 74935.914 Da / Num. of mol.: 2 / Fragment: UNP residues 1389-2016 / Mutation: D82N, E84Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 3.74 Å3/Da / Density % sol: 67.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2 M magnesium acetate tetrahydrate, 0.1 M sodium cacodylate trhydrate pH 6.5, 30% w/v polyethylene glycol 4000

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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: Jul 13, 2015
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: 44314 / % possible obs: 99.3 % / Redundancy: 3.5 % / Biso Wilson estimate: 54.05 Å2 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.056 / Rrim(I) all: 0.11 / Χ2: 1.405 / Net I/av σ(I): 14.884 / Net I/σ(I): 10.4 / Num. measured all: 155640
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.9-33.20.52643700.5990.3280.6250.9398.6
3-3.123.30.40444350.7380.2470.4770.96999.3
3.12-3.273.40.31744090.8370.1920.3741.04199.5
3.27-3.443.50.22244150.9320.1310.261.19199.6
3.44-3.653.50.1644410.9630.0950.1881.36999.6
3.65-3.943.60.11644310.980.0680.1351.53599.4
3.94-4.333.70.07444440.9910.0430.0861.5599.7
4.33-4.963.70.05844520.9940.0340.0681.76699.6
4.96-6.243.70.05744530.9940.0330.0661.76899.6
6.24-503.70.03244640.9980.0180.0371.72298.1

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Processing

Software
NameVersionClassification
PHENIX(1.10_2148: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
MR-Rosettaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DKT

5dkt


Resolution: 2.9→47.915 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2318 2007 4.53 %Random selection
Rwork0.1922 42264 --
obs0.194 44271 99.26 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 231.72 Å2 / Biso mean: 68.3285 Å2 / Biso min: 9.24 Å2
Refinement stepCycle: final / Resolution: 2.9→47.915 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9623 0 2 96 9721
Biso mean--63.16 33.26 -
Num. residues----1158
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029839
X-RAY DIFFRACTIONf_angle_d0.47713255
X-RAY DIFFRACTIONf_chiral_restr0.0431483
X-RAY DIFFRACTIONf_plane_restr0.0021685
X-RAY DIFFRACTIONf_dihedral_angle_d12.7576063
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 (%)
2.8993-2.97180.35561430.29672959310298
2.9718-3.05210.31771390.27763031317099
3.0521-3.14190.32921400.25642989312999
3.1419-3.24330.28931450.25230283173100
3.2433-3.35920.2741440.240530143158100
3.3592-3.49370.2471450.21923016316199
3.4937-3.65260.2731480.203130293177100
3.6526-3.84510.24531390.193130193158100
3.8451-4.08590.2111500.17413022317299
4.0859-4.40120.1671380.150130283166100
4.4012-4.84370.16651420.141230393181100
4.8437-5.54370.18811450.150730393184100
5.5437-6.9810.23471490.2033036318599
6.981-47.92130.22621400.17673015315597

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