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- PDB-2pjr: HELICASE PRODUCT COMPLEX -

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Basic information

Entry
Database: PDB / ID: 2pjr
TitleHELICASE PRODUCT COMPLEX
Components
  • (PROTEIN (HELICASE ...) x 2
  • DNA (5'-D(*AP*CP*TP*GP*C)-3')
  • DNA (5'-D(*GP*C)-3')
  • DNA (5'-D(*TP*TP*TP*TP*T)-3')
KeywordsHYDROLASE/DNA / HELICASE PCRA / HYDROLASE / DNA / PRODUCT COMPLEX / 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
Double Stranded RNA Binding Domain - #800 / 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 ...Double Stranded RNA Binding Domain - #800 / 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 / Double Stranded RNA Binding Domain / Arc Repressor Mutant, subunit A / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / ATP-dependent DNA helicase PcrA
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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 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
C: DNA (5'-D(*TP*TP*TP*TP*T)-3')
D: DNA (5'-D(*TP*TP*TP*TP*T)-3')
H: DNA (5'-D(*GP*C)-3')
I: DNA (5'-D(*AP*CP*TP*GP*C)-3')
A: PROTEIN (HELICASE PCRA)
B: PROTEIN (HELICASE PCRA)
F: PROTEIN (HELICASE PCRA)
G: PROTEIN (HELICASE PCRA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,36210
Polymers153,1708
Non-polymers1922
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.050, 62.600, 141.830
Angle α, β, γ (deg.)90.00, 95.84, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

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DNA chain , 3 types, 4 molecules CDHI

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


Mass: 1476.007 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*GP*C)-3')


Mass: 573.430 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*AP*CP*TP*GP*C)-3')


Mass: 1480.012 Da / Num. of mol.: 1 / Source method: obtained synthetically

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PROTEIN (HELICASE ... , 2 types, 4 molecules AFBG

#4: Protein PROTEIN (HELICASE PCRA) / EC 3.6.1.- / ATP-DEPENDENT HELICASE PCRA


Mass: 63369.156 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-548
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
#5: Protein PROTEIN (HELICASE PCRA) / EC 3.6.1.- / ATP-DEPENDENT HELICASE PCRA


Mass: 10713.169 Da / Num. of mol.: 2 / Fragment: RESIDUES 556-650
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

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Non-polymers , 1 types, 2 molecules

#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4

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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: 2.45 Å3/Da / Density % sol: 49.8 %
Crystal growpH: 8.5 / Details: pH 8.5
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Details: drop consists of 1:1 mixture of well and protein solutions
Components of the solutions
*PLUS
IDConc.UnitCommon nameCrystal-IDSol-IDChemical formula
8106 mM1dropNaCl
9100 mMTris-HCl1reservoir
1mMDNA substrate1drop
2%glucose1drop
4mMADPNP1drop
5mMdithiothreitol1drop
6mMTris-HCl1drop
7mMEDTA1drop
3mM1dropMgCl2
1050 mM1reservoirLi2SO4
1112-20 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.9→10 Å / Num. all: 31850 / Num. obs: 31850 / % possible obs: 97.9 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Rmerge(I) obs: 0.068

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Processing

SoftwareName: CNS / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→15 Å / Rfactor Rfree error: 0.007 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.296 1609 5.1 %
Rwork0.24 --
all-31850 -
obs-31850 97.9 %
Refinement stepCycle: LAST / Resolution: 2.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10333 330 10 0 10673
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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