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- PDB-7lw7: Human Exonuclease 5 crystal structure -

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Basic information

Entry
Database: PDB / ID: 7lw7
TitleHuman Exonuclease 5 crystal structure
ComponentsExonuclease VRecBCD
KeywordsHYDROLASE
Function / homology
Function and homology information


single-stranded DNA 5'-3' DNA exonuclease activity / single-stranded DNA 3'-5' DNA exonuclease activity / interstrand cross-link repair / 4 iron, 4 sulfur cluster binding / Hydrolases; Acting on ester bonds / DNA binding / nucleoplasm / metal ion binding / nucleus / cytosol
Similarity search - Function
Exonuclease V / Exonuclease V - a 5' deoxyribonuclease / PD-(D/E)XK endonuclease-like domain superfamily
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / Exonuclease V
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsTsai, C.L. / Tainer, J.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R35CA22043 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P01 CA092584 United States
CitationJournal: Mol.Cell / Year: 2021
Title: EXO5-DNA structure and BLM interactions direct DNA resection critical for ATR-dependent replication restart.
Authors: Hambarde, S. / Tsai, C.L. / Pandita, R.K. / Bacolla, A. / Maitra, A. / Charaka, V. / Hunt, C.R. / Kumar, R. / Limbo, O. / Le Meur, R. / Chazin, W.J. / Tsutakawa, S.E. / Russell, P. / ...Authors: Hambarde, S. / Tsai, C.L. / Pandita, R.K. / Bacolla, A. / Maitra, A. / Charaka, V. / Hunt, C.R. / Kumar, R. / Limbo, O. / Le Meur, R. / Chazin, W.J. / Tsutakawa, S.E. / Russell, P. / Schlacher, K. / Pandita, T.K. / Tainer, J.A.
History
DepositionFeb 27, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Mar 6, 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
A: Exonuclease V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6739
Polymers38,8571
Non-polymers8168
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.818, 83.836, 95.965
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Exonuclease V / RecBCD / Exo V / hExo5 / Defects in morphology protein 1 homolog


Mass: 38856.949 Da / Num. of mol.: 1 / Mutation: G145V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EXO5, C1orf176, DEM1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9H790, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.63 Å3/Da / Density % sol: 53.24 % / Description: needle
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350 and 0.2 M lithium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.1158 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionResolution: 2.5→47.983 Å / Num. obs: 14791 / % possible obs: 100 % / Redundancy: 6.4 % / CC1/2: 0.988 / Rmerge(I) obs: 0.246 / Rpim(I) all: 0.104 / Rrim(I) all: 0.267 / Net I/σ(I): 8.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.5-2.66.51.2631.616170.570.5311.373100
9.01-47.9835.40.046303750.9980.0210.05199.7

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.31data scaling
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→47.983 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2245 732 4.96 %
Rwork0.1821 14022 -
obs0.1842 14754 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 133.98 Å2 / Biso mean: 41.6189 Å2 / Biso min: 10.75 Å2
Refinement stepCycle: final / Resolution: 2.5→47.983 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2230 0 38 89 2357
Biso mean--49.78 38.26 -
Num. residues----277
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032316
X-RAY DIFFRACTIONf_angle_d0.5283131
X-RAY DIFFRACTIONf_chiral_restr0.043358
X-RAY DIFFRACTIONf_plane_restr0.003384
X-RAY DIFFRACTIONf_dihedral_angle_d7.3711376
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.5-2.6930.34851480.26772741
2.693-2.9640.26431400.23452755
2.964-3.39280.2561520.20392772
3.3928-4.27410.20451310.14712821
4.2741-47.9830.1691610.1542933

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