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- PDB-5aho: Crystal structure of human 5' exonuclease Apollo -

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Basic information

Entry
Database: PDB / ID: 5aho
TitleCrystal structure of human 5' exonuclease Apollo
Components5' EXONUCLEASE APOLLO
KeywordsHYDROLASE / DNA REPAIR METALLO-BETA-LACTAMASE / DCLRE1B
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 / 5'-3' exonuclease activity / telomere capping / 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 / 5'-3' exonuclease activity / telomere capping / 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 / chromosome, telomeric region / Hydrolases; Acting on ester bonds / nuclear body / centrosome / protein-containing complex binding / protein homodimerization activity / nucleoplasm / cytoplasm
Similarity search - Function
Rossmann fold - #12650 / DNA repair metallo-beta-lactamase / DNA repair metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
L(+)-TARTARIC ACID / 5' exonuclease Apollo
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsAllerston, C.K. / Vollmar, M. / Krojer, T. / Pike, A.C.W. / Newman, J.A. / Carpenter, E. / Quigley, A. / Mahajan, P. / von Delft, F. / Bountra, C. ...Allerston, C.K. / Vollmar, M. / Krojer, T. / Pike, A.C.W. / Newman, J.A. / Carpenter, E. / Quigley, A. / Mahajan, P. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / Gileadi, O.
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: The Structures of the Snm1A and Snm1B/Apollo Nuclease Domains Reveal a Potential Basis for Their Distinct DNA Processing Activities.
Authors: Allerston, C.K. / Lee, S.Y. / Newman, J.A. / Schofield, C.J. / Mchugh, P.J. / Gileadi, O.
History
DepositionFeb 6, 2015Deposition site: PDBE / Processing site: PDBE
SupersessionFeb 18, 2015ID: 3ZDK
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2016Group: Database references
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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

Downloads & links

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Assembly

Deposited unit
A: 5' EXONUCLEASE APOLLO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,70011
Polymers37,8971
Non-polymers80310
Water4,197233
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)143.092, 143.092, 143.092
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132

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Components

#1: Protein 5' EXONUCLEASE APOLLO / DNA CROSS-LINK REPAIR 1B PROTEIN / SNM1 HOMOLOG B / SNMIB / HSNM1B


Mass: 37896.645 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFB LIC BSE / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm)
References: UniProt: Q9H816, Hydrolases; Acting on ester bonds
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFIRST RESIDUE IS PART OF UNCLEAVED TAG.

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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: 3.22 Å3/Da / Density % sol: 61.82 % / Description: NONE
Crystal growDetails: 0.4M K/NA(TART)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.16→71.55 Å / Num. obs: 26072 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 18.4 % / Biso Wilson estimate: 31.07 Å2 / Rmerge(I) obs: 0.22 / Net I/σ(I): 12
Reflection shellResolution: 2.16→2.28 Å / Redundancy: 14.8 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1.9 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.16→50.591 Å / SU ML: 0.23 / σ(F): 1.34 / Phase error: 21.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2257 1362 5 %
Rwork0.2059 --
obs0.2069 27439 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.16→50.591 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2479 0 46 233 2758
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022624
X-RAY DIFFRACTIONf_angle_d0.5923568
X-RAY DIFFRACTIONf_dihedral_angle_d10.392944
X-RAY DIFFRACTIONf_chiral_restr0.024406
X-RAY DIFFRACTIONf_plane_restr0.003455
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1601-2.23730.32461410.31042551X-RAY DIFFRACTION100
2.2373-2.32690.30371230.27562545X-RAY DIFFRACTION100
2.3269-2.43280.25561340.25432566X-RAY DIFFRACTION100
2.4328-2.56110.27311390.25282562X-RAY DIFFRACTION100
2.5611-2.72150.26591180.23872571X-RAY DIFFRACTION100
2.7215-2.93160.26161300.23782585X-RAY DIFFRACTION100
2.9316-3.22660.24651690.21212565X-RAY DIFFRACTION100
3.2266-3.69340.20061420.19342621X-RAY DIFFRACTION100
3.6934-4.65280.18851380.15942660X-RAY DIFFRACTION100
4.6528-50.60450.18051280.17262851X-RAY DIFFRACTION100

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