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- PDB-7a1f: Crystal structure of human 5' exonuclease Appollo in complex with... -

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Basic information

Entry
Database: PDB / ID: 7a1f
TitleCrystal structure of human 5' exonuclease Appollo in complex with 5'dAMP
Components5' exonuclease Apollo
KeywordsLYASE / DCLRE1B / SNM1B / exonuclease / Apollo
Function / homology
Function and homology information


telomeric 3' overhang formation / telomeric loop formation / protection from non-homologous end joining at telomere / telomere maintenance via telomere lengthening / telomere capping / 5'-3' exonuclease activity / 5'-3' DNA exonuclease activity / interstrand cross-link repair / telomere maintenance / Fanconi Anemia Pathway ...telomeric 3' overhang formation / telomeric loop formation / protection from non-homologous end joining at telomere / telomere maintenance via telomere lengthening / telomere capping / 5'-3' exonuclease activity / 5'-3' DNA exonuclease activity / interstrand cross-link repair / telomere maintenance / Fanconi Anemia Pathway / beta-lactamase activity / double-strand break repair via nonhomologous end joining / beta-lactamase / damaged DNA binding / Hydrolases; Acting on ester bonds / chromosome, telomeric region / nuclear body / centrosome / protein-containing complex binding / protein homodimerization activity / nucleoplasm / cytoplasm
Similarity search - Function
DNA repair metallo-beta-lactamase / DNA repair metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE / : / NICKEL (II) ION / 5' exonuclease Apollo
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsNewman, J.A. / Baddock, H.T. / Mukhopadhyay, S.M.M. / Burgess-Brown, N.A. / von Delft, F. / Arrowshmith, C.H. / Edwards, A. / Bountra, C. / Gileadi, O.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UK United Kingdom
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: A phosphate binding pocket is a key determinant of exo- versus endo-nucleolytic activity in the SNM1 nuclease family.
Authors: Baddock, H.T. / Newman, J.A. / Yosaatmadja, Y. / Bielinski, M. / Schofield, C.J. / Gileadi, O. / McHugh, P.J.
History
DepositionAug 12, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5' exonuclease Apollo
L: 5' exonuclease Apollo
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,86910
Polymers77,3152
Non-polymers1,5548
Water10,196566
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-71 kcal/mol
Surface area29940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.121, 54.183, 72.109
Angle α, β, γ (deg.)75.480, 74.330, 63.090
Int Tables number1
Space group name H-MP1

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Components

#1: Protein 5' exonuclease Apollo / DNA cross-link repair 1B protein / SNM1 homolog B / hSNM1B


Mass: 38657.434 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DCLRE1B, SNM1B / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9H816, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Chemical
ChemComp-D5M / 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE


Mass: 331.222 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O6P / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 566 / 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: 2.15 Å3/Da / Density % sol: 42.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 0.2M Ammonium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→68.65 Å / Num. obs: 55714 / % possible obs: 93.3 % / Redundancy: 2.2 % / Biso Wilson estimate: 23.76 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.051 / Rrim(I) all: 0.081 / Net I/σ(I): 7.9 / Num. measured all: 123105 / Scaling rejects: 3
Reflection shell

Diffraction-ID: 1 / Redundancy: 2.3 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.8-1.840.622762233680.6520.5160.8121.395.5
9-68.650.02510254480.9860.020.03225.495.1

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Processing

Software
NameVersionClassification
Aimless0.5.31data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5AHO

5aho


Resolution: 1.8→43.953 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 27.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2226 2823 5.07 %
Rwork0.1773 52859 -
obs0.1796 55682 93.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.6 Å2 / Biso mean: 31.9746 Å2 / Biso min: 13.27 Å2
Refinement stepCycle: final / Resolution: 1.8→43.953 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5247 0 38 566 5851
Biso mean--40.44 37.85 -
Num. residues----667
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075488
X-RAY DIFFRACTIONf_angle_d0.9037495
X-RAY DIFFRACTIONf_chiral_restr0.055854
X-RAY DIFFRACTIONf_plane_restr0.006938
X-RAY DIFFRACTIONf_dihedral_angle_d13.3573223
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8-1.8310.39581390.3262270696
1.831-1.86430.32571420.2886273095
1.8643-1.90020.3141480.2761268996
1.9002-1.9390.2881750.2634182763
1.939-1.98110.31061420.2444269496
1.9811-2.02720.32761200.2297274996
2.0272-2.07790.30661090.2381208173
2.0779-2.13410.26561420.2119271397
2.1341-2.19690.27141800.1967274497
2.1969-2.26780.26351370.1937221579
2.2678-2.34890.27571140.1889276397
2.3489-2.44290.25021330.1914274597
2.4429-2.55410.24911510.1885275998
2.5541-2.68870.24481570.1849277098
2.6887-2.85710.2191650.1847278798
2.8571-3.07770.20831810.1793273098
3.0777-3.38730.23431590.1757278598
3.3873-3.87720.20911250.1486282598
3.8772-4.88380.13871260.1277279598
4.8838-43.9530.16051780.139275298

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