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- PDB-2e6l: structure of mouse WRN exonuclease domain -

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Basic information

Entry
Database: PDB / ID: 2e6l
Titlestructure of mouse WRN exonuclease domain
ComponentsWerner syndrome ATP-dependent helicase homolog
KeywordsHYDROLASE / Zn-protein complex
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 / G2/M DNA damage checkpoint / 3'-flap-structured DNA binding / positive regulation of strand invasion / HDR through Single Strand Annealing (SSA) / HDR through Homologous Recombination (HRR) ...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 / G2/M DNA damage checkpoint / 3'-flap-structured DNA binding / positive regulation of strand invasion / HDR through Single Strand Annealing (SSA) / HDR through Homologous Recombination (HRR) / Processing of DNA double-strand break ends / forked DNA-dependent helicase activity / telomeric G-quadruplex DNA binding / 8-hydroxy-2'-deoxyguanosine DNA binding / telomeric D-loop binding / regulation of growth rate / DNA geometric change / Y-form DNA binding / telomeric D-loop disassembly / Regulation of TP53 Activity through Phosphorylation / four-way junction helicase activity / G-quadruplex DNA binding / bubble DNA binding / MutLalpha complex binding / protein localization to nucleolus / response to UV-C / exonuclease activity / DNA metabolic process / DNA synthesis involved in DNA repair / 3'-5' DNA helicase activity / DNA 3'-5' helicase / replication fork processing / replicative senescence / mismatch repair / four-way junction DNA binding / 3'-5' exonuclease activity / DNA helicase activity / telomere maintenance / cellular response to starvation / replication fork / determination of adult lifespan / cellular response to gamma radiation / double-strand break repair via homologous recombination / base-excision repair / cellular senescence / double-strand break repair / manganese ion binding / chromosome / response to oxidative stress / regulation of apoptotic process / Hydrolases; Acting on ester bonds / DNA replication / chromosome, telomeric region / nuclear speck / DNA damage response / chromatin binding / centrosome / protein-containing complex binding / nucleolus / magnesium ion binding / protein homodimerization activity / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / nucleus / cytoplasm
Similarity search - Function
Helicase Helix-turn-helix domain / Helix-turn-helix domain / RQC domain / RQC / RQC domain / Helicase and RNase D C-terminal / ATP-dependent DNA helicase RecQ, zinc-binding domain / RecQ zinc-binding / HRDC domain / HRDC domain ...Helicase Helix-turn-helix domain / Helix-turn-helix domain / RQC domain / RQC / RQC domain / Helicase and RNase D C-terminal / ATP-dependent DNA helicase RecQ, zinc-binding domain / RecQ zinc-binding / HRDC domain / HRDC domain / DNA helicase, ATP-dependent, RecQ type / HRDC domain profile. / 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 / MAD / Resolution: 2.2 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 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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)23,6294
Polymers23,4021
Non-polymers2273
Water2,702150
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.047, 59.147, 60.245
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: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.28 %
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

Diffraction
IDMean temperature (K)Crystal-ID
193.151
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPAL/PLS 4A11.2835
SYNCHROTRONPAL/PLS 4A21.2831, 1.2825, 1.2699
Detector
IDDetectorDate
1CCDFeb 14, 2005
2CCDFeb 14, 2005
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.28351
21.28311
31.28251
41.26991
ReflectionResolution: 2.2→50 Å / Num. all: 11712 / Num. obs: 11712 / % possible obs: 99.5 % / Redundancy: 4.5 % / Biso Wilson estimate: 9.4 Å2 / Rsym value: 0.076 / Net I/σ(I): 40
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 40 / Num. unique all: 11712 / Rsym value: 0.076 / % possible all: 99.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→29.57 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 67763.48 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.244 531 5.1 %RANDOM
Rwork0.197 ---
obs0.197 10377 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.0364 Å2 / ksol: 0.404775 e/Å3
Displacement parametersBiso mean: 24.9 Å2
Baniso -1Baniso -2Baniso -3
1--1.65 Å20 Å20 Å2
2---3.43 Å20 Å2
3---5.08 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a-0.05 Å
Refinement stepCycle: LAST / Resolution: 2.2→29.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1465 0 7 150 1622
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d0.69
X-RAY DIFFRACTIONc_mcbond_it1.391.5
X-RAY DIFFRACTIONc_mcangle_it2.192
X-RAY DIFFRACTIONc_scbond_it2.372
X-RAY DIFFRACTIONc_scangle_it3.342.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.225 83 5 %
Rwork0.184 1592 -
obs--98.7 %
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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