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- PDB-3lfu: Crystal Structure of E. coli UvrD -

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Basic information

Entry
Database: PDB / ID: 3lfu
TitleCrystal Structure of E. coli UvrD
ComponentsDNA helicase IIHelicase
KeywordsHYDROLASE / DNA helicase / SF1 helicase / ATP-binding / DNA damage / DNA repair / DNA replication / DNA-binding / Helicase / Nucleotide-binding / SOS response
Function / homology
Function and homology information


rolling circle DNA replication / single-stranded DNA-dependent ATP-dependent DNA helicase complex / mismatch repair involved in maintenance of fidelity involved in DNA-dependent DNA replication / DNA helicase complex / nucleotide-excision repair, DNA duplex unwinding / DNA 3'-5' helicase / DNA translocase activity / recombinational repair / single-stranded DNA helicase activity / DNA duplex unwinding ...rolling circle DNA replication / single-stranded DNA-dependent ATP-dependent DNA helicase complex / mismatch repair involved in maintenance of fidelity involved in DNA-dependent DNA replication / DNA helicase complex / nucleotide-excision repair, DNA duplex unwinding / DNA 3'-5' helicase / DNA translocase activity / recombinational repair / single-stranded DNA helicase activity / DNA duplex unwinding / 3'-5' DNA helicase activity / replication fork processing / DNA unwinding involved in DNA replication / SOS response / mismatch repair / isomerase activity / DNA helicase activity / nucleotide-excision repair / response to radiation / protein homodimerization activity / ATP hydrolysis activity / DNA binding / ATP binding / cytosol
Similarity search - Function
DNA helicase, ATP-dependent, UvrD type / PcrA/UvrD tudor domain / 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 ...DNA helicase, ATP-dependent, UvrD type / PcrA/UvrD tudor domain / 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
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsKorolev, S. / Waksman, G. / Lohman, T.M.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Rotations of the 2B sub-domain of E. coli UvrD helicase/translocase coupled to nucleotide and DNA binding.
Authors: Jia, H. / Korolev, S. / Niedziela-Majka, A. / Maluf, N.K. / Gauss, G.H. / Myong, S. / Ha, T. / Waksman, G. / Lohman, T.M.
History
DepositionJan 18, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 30, 2011Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type / _software.version
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: DNA helicase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,4695
Polymers74,0851
Non-polymers3844
Water12,989721
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)194.543, 58.739, 69.418
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein DNA helicase II / Helicase


Mass: 74084.773 Da / Num. of mol.: 1 / Fragment: C-terminal truncation (UNP residues 1-647)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: b3813, JW3786, mutU, pdeB, rad, recL, uvrD / Production host: Escherichia coli (E. coli)
References: UniProt: P03018, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 721 / 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: 2.68 Å3/Da / Density % sol: 54.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.1
Details: 1.0 M (NH4)2SO4, pH 9.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.99188 Å
DetectorType: SBC-2 / Detector: CCD / Date: Mar 10, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99188 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 70609 / % possible obs: 94 % / Observed criterion σ(F): 1 / Rsym value: 0.064
Reflection shellResolution: 1.8→1.83 Å / Rsym value: 0.224 / % possible all: 86

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0102refinement
CNSrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→29.54 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.923 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.73 / SU ML: 0.087 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.248 3393 5 %RANDOM
Rwork0.199 ---
obs0.202 67970 90.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 83.23 Å2 / Biso mean: 25.754 Å2 / Biso min: 4.36 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5039 0 20 721 5780
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0215143
X-RAY DIFFRACTIONr_angle_refined_deg1.7631.9546944
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8025628
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.09223.509265
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.2615903
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2331554
X-RAY DIFFRACTIONr_chiral_restr0.180.2751
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0213932
X-RAY DIFFRACTIONr_mcbond_it1.5541.53132
X-RAY DIFFRACTIONr_mcangle_it2.57724987
X-RAY DIFFRACTIONr_scbond_it4.28432011
X-RAY DIFFRACTIONr_scangle_it6.2974.51957
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 250 -
Rwork0.27 5193 -
all-5443 -
obs--99.98 %

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