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- PDB-3pjr: HELICASE SUBSTRATE COMPLEX -

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Basic information

Entry
Database: PDB / ID: 3pjr
TitleHELICASE SUBSTRATE COMPLEX
Components
  • 5'-D(*CP*GP*AP*GP*CP*AP*CP*TP*GP*C)-3'
  • 5'-D(*GP*CP*AP*GP*TP*GP*CP*TP*CP*GP*TP*TP*TP*TP*T)-3'
  • HELICASE PCRA
KeywordsHYDROLASE/DNA / HELICASE / HYDROLASE-DNA COMPLEX
Function / homology
Function and homology information


DNA helicase complex / recombinational repair / DNA 3'-5' helicase / 3'-5' DNA helicase activity / DNA replication / ATP hydrolysis activity / DNA binding / ATP binding / cytosol
Similarity search - Function
ATP-dependent DNA helicase PcrA / Arc Repressor Mutant, subunit A - #160 / PcrA/UvrD tudor domain / PCRA; domain 4 / PCRA; domain 4 / DExx box DNA helicase domain superfamily / UvrD-like DNA helicase C-terminal domain profile. / UvrD-like DNA helicase, C-terminal / UvrD-like helicase C-terminal domain / UvrD/REP helicase N-terminal domain ...ATP-dependent DNA helicase PcrA / Arc Repressor Mutant, subunit A - #160 / PcrA/UvrD tudor domain / PCRA; domain 4 / PCRA; domain 4 / DExx box DNA helicase domain superfamily / UvrD-like DNA helicase C-terminal domain profile. / UvrD-like DNA helicase, C-terminal / UvrD-like helicase C-terminal domain / UvrD/REP helicase N-terminal domain / UvrD-like DNA helicase ATP-binding domain profile. / DNA helicase, UvrD/REP type / UvrD-like helicase, ATP-binding domain / Arc Repressor Mutant, subunit A / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / ATP-dependent DNA helicase PcrA
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsVelankar, S.S. / Soultanas, P. / Dillingham, M.S. / Subramanya, H.S. / Wigley, D.B.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1999
Title: Crystal structures of complexes of PcrA DNA helicase with a DNA substrate indicate an inchworm mechanism
Authors: Velankar, S.S. / Soultanas, P. / Dillingham, M.S. / Subramanya, H.S. / Wigley, D.B.
History
DepositionMar 12, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Apr 8, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 28, 2011Group: Advisory
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
Y: 5'-D(*GP*CP*AP*GP*TP*GP*CP*TP*CP*GP*TP*TP*TP*TP*T)-3'
Z: 5'-D(*CP*GP*AP*GP*CP*AP*CP*TP*GP*C)-3'
A: HELICASE PCRA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,7144
Polymers90,2073
Non-polymers5071
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.120, 105.120, 380.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Cell settinghexagonal
Space group name H-MP6122

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Components

#1: DNA chain 5'-D(*GP*CP*AP*GP*TP*GP*CP*TP*CP*GP*TP*TP*TP*TP*T)-3'


Mass: 4581.967 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*CP*GP*AP*GP*CP*AP*CP*TP*GP*C)-3'


Mass: 3029.994 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein HELICASE PCRA / EC 3.6.1.-


Mass: 82595.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Production host: Escherichia coli (E. coli)
References: UniProt: P56255, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM

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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: 3.36 Å3/Da / Density % sol: 63.34 %
Crystal growpH: 8.5 / Details: pH 8.5
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop / Details: used to seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.175 mMDNA1drop
24.8 %glucose1drop
35 mM1dropMgCl2
42.5 mMADPNP1drop
52 mMdithiothreitol1drop
626.5 mMTris1drop
71 mMEDTA1drop
8106 mM1dropNaCl
9100 mMTris1reservoir
1050 mM1reservoirLiSO4
1112-20 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9
DetectorDetector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.3→10 Å / Num. all: 17365 / Num. obs: 17365 / % possible obs: 92 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.06
Reflection
*PLUS
% possible obs: 92 % / Rmerge(I) obs: 0.06

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Processing

SoftwareName: REFMAC / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→10 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.315 -5 %
Rwork0.236 --
all-17365 -
obs-17365 92 %
Refinement stepCycle: LAST / Resolution: 3.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5230 504 31 0 5765
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.014
X-RAY DIFFRACTIONp_angle_d0.026
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 3.3 Å / Lowest resolution: 10 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.236
Solvent computation
*PLUS
Displacement parameters
*PLUS

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