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- PDB-2e6m: structure of mouse werner exonuclease domain -

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Basic information

Entry
Database: PDB / ID: 2e6m
Titlestructure of mouse werner exonuclease domain
ComponentsWerner syndrome ATP-dependent helicase homolog
KeywordsHYDROLASE / apo form
Function / homology
Function and homology information


Processive synthesis on the C-strand of the telomere / Removal of the Flap Intermediate from the C-strand / Presynaptic phase of homologous DNA pairing and strand exchange / Homologous DNA Pairing and Strand Exchange / Resolution of D-loop Structures through Holliday Junction Intermediates / 3'-flap-structured DNA binding / positive regulation of strand invasion / HDR through Single Strand Annealing (SSA) / HDR through Homologous Recombination (HRR) / G2/M DNA damage checkpoint ...Processive synthesis on the C-strand of the telomere / Removal of the Flap Intermediate from the C-strand / Presynaptic phase of homologous DNA pairing and strand exchange / Homologous DNA Pairing and Strand Exchange / Resolution of D-loop Structures through Holliday Junction Intermediates / 3'-flap-structured DNA binding / positive regulation of strand invasion / HDR through Single Strand Annealing (SSA) / HDR through Homologous Recombination (HRR) / G2/M DNA damage checkpoint / telomeric G-quadruplex DNA binding / 8-hydroxy-2'-deoxyguanosine DNA binding / telomeric D-loop binding / Processing of DNA double-strand break ends / regulation of growth rate / telomeric D-loop disassembly / DNA geometric change / Y-form DNA binding / Regulation of TP53 Activity through Phosphorylation / bubble DNA binding / MutLalpha complex binding / protein localization to nucleolus / response to UV-C / exonuclease activity / DNA 3'-5' helicase / DNA metabolic process / DNA synthesis involved in DNA repair / replication fork processing / replicative senescence / DNA helicase activity / four-way junction DNA binding / 3'-5' exonuclease activity / telomere maintenance / cellular response to starvation / replication fork / determination of adult lifespan / isomerase activity / cellular response to gamma radiation / base-excision repair / cellular senescence / double-strand break repair / manganese ion binding / regulation of apoptotic process / DNA recombination / response to oxidative stress / Hydrolases; Acting on ester bonds / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / chromosome, telomeric region / DNA replication / nuclear speck / centrosome / chromatin binding / nucleolus / magnesium ion binding / protein homodimerization activity / ATP hydrolysis activity / nucleoplasm / ATP binding / nucleus
Similarity search - Function
Helicase Helix-turn-helix domain / Helix-turn-helix domain / RQC domain / RQC / RQC domain / Helicase and RNase D C-terminal / HRDC domain / HRDC domain / HRDC domain profile. / ATP-dependent DNA helicase RecQ, zinc-binding domain ...Helicase Helix-turn-helix domain / Helix-turn-helix domain / RQC domain / RQC / RQC domain / Helicase and RNase D C-terminal / HRDC domain / HRDC domain / HRDC domain profile. / ATP-dependent DNA helicase RecQ, zinc-binding domain / RecQ zinc-binding / DNA helicase, ATP-dependent, RecQ type / HRDC domain superfamily / 3'-5' exonuclease / 3'-5' exonuclease / 3'-5' exonuclease domain / HRDC-like superfamily / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Ribonuclease H-like superfamily/Ribonuclease H / Helicase conserved C-terminal domain / Nucleotidyltransferase; domain 5 / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Bifunctional 3'-5' exonuclease/ATP-dependent helicase WRN
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCho, Y. / Choi, J.M.
CitationJournal: TO BE PUBLISHED
Title: probing the roles of active site residues in 3'-5' exonuclease of werner syndrome protein
Authors: Cho, Y. / Choi, J.M.
History
DepositionDec 27, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 16, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: Werner syndrome ATP-dependent helicase homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4982
Polymers23,4021
Non-polymers961
Water2,252125
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.925, 59.189, 60.466
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Werner syndrome ATP-dependent helicase homolog


Mass: 23401.854 Da / Num. of mol.: 1 / Fragment: wrn exonuclease domain, residues 31-238
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Wrn / Plasmid: pET-28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O09053, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.1 Å3/Da / Density % sol: 41.41 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K

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Data collection

DiffractionMean temperature: 93.15 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorDetector: CCD / Date: Feb 14, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 14814 / Num. obs: 14814 / % possible obs: 96 % / Redundancy: 5.2 % / Biso Wilson estimate: 7 Å2 / Rsym value: 0.092 / Net I/σ(I): 29
Reflection shellResolution: 2→2.11 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 29 / Num. unique all: 14814 / Rsym value: 0.092 / % possible all: 96

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2E6L

2e6l


Resolution: 2→29.6 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 77755.73 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.243 652 5 %RANDOM
Rwork0.209 ---
obs0.209 13095 94.5 %-
all-14814 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.3719 Å2 / ksol: 0.390643 e/Å3
Displacement parametersBiso mean: 25 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2---6.57 Å20 Å2
3---6.51 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2→29.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1465 0 5 125 1595
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d0.68
X-RAY DIFFRACTIONc_mcbond_it1.51.5
X-RAY DIFFRACTIONc_mcangle_it2.22
X-RAY DIFFRACTIONc_scbond_it2.432
X-RAY DIFFRACTIONc_scangle_it3.482.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.287 104 4.9 %
Rwork0.247 2000 -
obs--92.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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