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- PDB-3ulp: Plasmodium falciparum SSB complex with ssDNA -

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Basic information

Entry
Database: PDB / ID: 3ulp
TitlePlasmodium falciparum SSB complex with ssDNA
Components
  • DNA (35-MER)
  • Single-strand binding protein
KeywordsDNA BINDING PROTEIN/DNA / OB-fold / DNA binding / single-stranded DNA / apicoplast / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


positive regulation of mitochondrial DNA replication / apicoplast / : / mitochondrial nucleoid / enzyme activator activity / single-stranded DNA binding / DNA replication
Similarity search - Function
Single-stranded DNA-binding protein / Single-strand binding protein family / Single-strand binding (SSB) domain profile. / Primosome PriB/single-strand DNA-binding / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Single-stranded DNA-binding protein
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Synthetic DNA (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsAntony, E. / Lohman, T.M. / Korolev, S.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Plasmodium falciparum SSB Tetramer Wraps Single-Stranded DNA with Similar Topology but Opposite Polarity to E. coli SSB.
Authors: Antony, E. / Weiland, E.A. / Korolev, S. / Lohman, T.M.
History
DepositionNov 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Single-strand binding protein
B: Single-strand binding protein
C: Single-strand binding protein
D: Single-strand binding protein
R: DNA (35-MER)
Q: DNA (35-MER)


Theoretical massNumber of molelcules
Total (without water)79,7506
Polymers79,7506
Non-polymers00
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20700 Å2
ΔGint-75 kcal/mol
Surface area25530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.017, 82.794, 87.556
Angle α, β, γ (deg.)90.00, 99.57, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-229-

HOH

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Components

#1: Protein
Single-strand binding protein


Mass: 14636.719 Da / Num. of mol.: 4 / Fragment: UNP residues 77-200
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: PFE0435c / Production host: Escherichia coli (E. coli) / References: UniProt: Q8I415
#2: DNA chain DNA (35-MER)


Mass: 10601.791 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Synthetic DNA (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 2.64 Å3/Da / Density % sol: 53.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Bis-Tris Propane, pH 8.5, 20 % PEG 3350, 0.2 M sodium bromide, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 21, 2011
RadiationMonochromator: VHF optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 48456 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Rmerge(I) obs: 0.068
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 3 % / Rmerge(I) obs: 0.529 / Mean I/σ(I) obs: 2.8 / Num. unique all: 2375 / % possible all: 97.3

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASESphasing
ARP/wARPmodel building
Cootmodel building
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EQQ

1eqq


Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.911 / SU B: 5.001 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27557 2438 5.1 %RANDOM
Rwork0.21795 ---
obs0.22084 45791 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.239 Å2
Baniso -1Baniso -2Baniso -3
1-1.1 Å20 Å20.03 Å2
2--0.73 Å20 Å2
3----1.82 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3638 1000 0 228 4866
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224812
X-RAY DIFFRACTIONr_angle_refined_deg1.4682.2166693
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.2575447
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.69123.892167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.65415691
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6681528
X-RAY DIFFRACTIONr_chiral_restr0.1110.2770
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.023201
X-RAY DIFFRACTIONr_mcbond_it2.2331.52252
X-RAY DIFFRACTIONr_mcangle_it3.73123617
X-RAY DIFFRACTIONr_scbond_it4.72732560
X-RAY DIFFRACTIONr_scangle_it6.5544.53076
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 185 -
Rwork0.283 3372 -
obs--99.16 %

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