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- PDB-1uaa: E. COLI REP HELICASE/DNA COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1uaa
TitleE. COLI REP HELICASE/DNA COMPLEX
Components
  • DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
  • PROTEIN (ATP-DEPENDENT DNA HELICASE REP.)
KeywordsHYDROLASE/DNA / COMPLEX (HELICASE-DNA) / HELICASE / DNA UNWINDING / HYDROLASE-DNA COMPLEX
Function / homology
Function and homology information


bacterial-type DNA replication / recombinational repair / 3'-5' DNA helicase activity / DNA unwinding involved in DNA replication / 3'-5' exonuclease activity / DNA helicase activity / response to radiation / single-stranded DNA binding / DNA helicase / DNA repair ...bacterial-type DNA replication / recombinational repair / 3'-5' DNA helicase activity / DNA unwinding involved in DNA replication / 3'-5' exonuclease activity / DNA helicase activity / response to radiation / single-stranded DNA binding / DNA helicase / DNA repair / ATP binding / cytosol
Similarity search - Function
ATP-dependent DNA helicase Rep / : / Arc Repressor Mutant, subunit A - #160 / 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 Rep / : / Arc Repressor Mutant, subunit A - #160 / 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 helicase, ATP-binding domain / UvrD-like DNA helicase ATP-binding domain profile. / DNA helicase, UvrD/REP type / Arc Repressor Mutant, subunit A / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / ATP-dependent DNA helicase Rep
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å
AuthorsKorolev, S. / Waksman, G.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1997
Title: Major domain swiveling revealed by the crystal structures of complexes of E. coli Rep helicase bound to single-stranded DNA and ADP.
Authors: Korolev, S. / Hsieh, J. / Gauss, G.H. / Lohman, T.M. / Waksman, G.
History
DepositionJun 30, 1997Deposition site: BNL / Processing site: NDB
Revision 1.0Jul 9, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
C: DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
A: PROTEIN (ATP-DEPENDENT DNA HELICASE REP.)
B: PROTEIN (ATP-DEPENDENT DNA HELICASE REP.)


Theoretical massNumber of molelcules
Total (without water)158,9063
Polymers158,9063
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)141.800, 141.800, 284.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 4822.127 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
#2: Protein PROTEIN (ATP-DEPENDENT DNA HELICASE REP.) / E.C.3.6.1.- / REP HELICASE


Mass: 77042.078 Da / Num. of mol.: 2 / Source method: obtained synthetically
References: UniProt: P09980, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.5 Å3/Da / Density % sol: 70 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8 / Details: pH 8.00, VAPOR DIFFUSION, temperature 293.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2NACLSodium chloride11
3TRIS-HCLTris11
4EDTAEthylenediaminetetraacetic acid11
5GLYCEROL11
6WATER12
7GLYCEROL12
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 %(v/v)glycerol1drop
20.1 M1dropNaCl
350 mMTris-HCl1drop
41 mM1drop
520 mg/mlprotain1drop
62.5 %PEG80001drop
72 %(v/v)glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 7, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 57472 / % possible obs: 97.3 % / Redundancy: 7 % / Rmerge(I) obs: 0.053
Reflection
*PLUS
Highest resolution: 3 Å / Lowest resolution: 30 Å / % possible obs: 97.3 % / Num. measured all: 434546

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Processing

Software
NameVersionClassification
DENZOdata reduction
X-PLOR3.1refinement
RefinementResolution: 3→15 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.328 --
Rwork0.228 --
obs-51675 88 %
Displacement parametersBiso mean: 41 Å2
Refinement stepCycle: LAST / Resolution: 3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10087 317 0 0 10404
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
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_deg1.92
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
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 15 Å / σ(I): 2 / Rfactor all: 0.235 / Rfactor obs: 0.228
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 41 Å2
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 1.918

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