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- PDB-1exn: T5 5'-EXONUCLEASE -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1exn
TitleT5 5'-EXONUCLEASE
Components5'-EXONUCLEASE
KeywordsNUCLEASE / HYDROLASE / EXONUCLEASE
Function / homology
Function and homology information


viral replication complex / exodeoxyribonuclease (lambda-induced) / late viral transcription / DNA replication, Okazaki fragment processing / double-stranded DNA 5'-3' DNA exonuclease activity / double-stranded DNA endonuclease activity / DNA exonuclease activity / 5'-flap endonuclease activity / viral DNA genome replication / 5'-3' exonuclease activity ...viral replication complex / exodeoxyribonuclease (lambda-induced) / late viral transcription / DNA replication, Okazaki fragment processing / double-stranded DNA 5'-3' DNA exonuclease activity / double-stranded DNA endonuclease activity / DNA exonuclease activity / 5'-flap endonuclease activity / viral DNA genome replication / 5'-3' exonuclease activity / 5'-3' DNA exonuclease activity / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / DNA binding / metal ion binding
Similarity search - Function
Flap endonuclease D15-like / Flap endonuclease / 5'-nuclease / DNA polymerase I-like, H3TH domain / 5'-3' exonuclease, C-terminal SAM fold / 5'-3' exonuclease, alpha-helical arch, N-terminal / 5'-3' exonuclease, N-terminal resolvase-like domain / 5'-3' exonuclease / 5'-3' exonuclease / Helix-hairpin-helix motif, class 2 ...Flap endonuclease D15-like / Flap endonuclease / 5'-nuclease / DNA polymerase I-like, H3TH domain / 5'-3' exonuclease, C-terminal SAM fold / 5'-3' exonuclease, alpha-helical arch, N-terminal / 5'-3' exonuclease, N-terminal resolvase-like domain / 5'-3' exonuclease / 5'-3' exonuclease / Helix-hairpin-helix motif, class 2 / Helix-hairpin-helix class 2 (Pol1 family) motifs / 5'-3' exonuclease, C-terminal domain superfamily / PIN-like domain superfamily / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesEnterobacteria phage T5 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsCeska, T.A. / Sayers, J.R. / Stier, G. / Suck, D.
Citation
Journal: Nature / Year: 1996
Title: A helical arch allowing single-stranded DNA to thread through T5 5'-exonuclease.
Authors: Ceska, T.A. / Sayers, J.R. / Stier, G. / Suck, D.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Preliminary Crystallographic Studies on the D15 5' to 3' Exonuclease from Phage T5
Authors: Ceska, T.A. / Sayers, J.R. / Eckstein, F. / Suck, D.
#2: Journal: J.Biol.Chem. / Year: 1990
Title: Properties of Overexpressed Phage T5 D15 Exonuclease. Similarities with Escherichia Coli DNA Polymerase I 5'-3' Exonuclease
Authors: Sayers, J.R. / Eckstein, F.
History
DepositionJan 17, 1997Processing site: BNL
Revision 1.0Jul 7, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 11, 2018Group: Data collection / Other / Category: pdbx_database_status / Item: _pdbx_database_status.process_site
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-EXONUCLEASE
B: 5'-EXONUCLEASE


Theoretical massNumber of molelcules
Total (without water)67,1902
Polymers67,1902
Non-polymers00
Water4,071226
1
A: 5'-EXONUCLEASE


Theoretical massNumber of molelcules
Total (without water)33,5951
Polymers33,5951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 5'-EXONUCLEASE


Theoretical massNumber of molelcules
Total (without water)33,5951
Polymers33,5951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.760, 77.760, 134.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein 5'-EXONUCLEASE / 5'-NUCLEASE / 5'-3' EXONUCLEASE


Mass: 33595.141 Da / Num. of mol.: 2 / Mutation: SEMET LABELLED PROTEIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T5 (virus) / Genus: T5-like viruses / Gene: D15 / Plasmid: PDOC55 / Gene (production host): D15 / Production host: Escherichia coli (E. coli) / Strain (production host): LE392
References: UniProt: P06229, exodeoxyribonuclease (lambda-induced)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE N-TERMINAL MET IS REMOVED IN E. COLI. THE GENE SEQUENCE STARTING FROM RESIDUE 1 IS USED AS THE ...THE N-TERMINAL MET IS REMOVED IN E. COLI. THE GENE SEQUENCE STARTING FROM RESIDUE 1 IS USED AS THE NUMBERING SEQUENCE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.03 Å3/Da / Density % sol: 60 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Ceska, T.A., (1993) J.Mol.Biol., 233, 179. / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mg/mlprotein1drop
2100 mMsodium citrate1reservoir
335 %(w/v)ammonium sulfate1reservoir
425 mMpotassium phosphate1droppH7.5
51 mMEDTA1drop
61 mMdithiothreitol1drop
7100 mM1dropKCl
85 %(v/v)glycerol1drop

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BL19 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 26, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionNum. obs: 26463 / % possible obs: 95.2 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.037
Reflection
*PLUS
Highest resolution: 2.5 Å / Num. measured all: 67552

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.5→6 Å / σ(F): 0 / Details: RESIDUE GLU A 290 IS IN POORLY DEFINED DENSITY.
RfactorNum. reflection% reflection
Rfree0.339 -10 %
Rwork0.227 --
obs0.227 24524 -
Refinement stepCycle: LAST / Resolution: 2.5→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4398 0 0 226 4624
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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