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- PDB-1ut8: Divalent metal ions (zinc) bound to T5 5'-exonuclease -

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Basic information

Entry
Database: PDB / ID: 1ut8
TitleDivalent metal ions (zinc) bound to T5 5'-exonuclease
ComponentsEXODEOXYRIBONUCLEASE
KeywordsHYDROLASE / EXONUCLEASE / NUCLEASE
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 / DNA exonuclease activity / double-stranded DNA endonuclease activity / 5'-flap endonuclease activity / 5'-3' exonuclease activity / viral DNA genome replication ...viral replication complex / exodeoxyribonuclease (lambda-induced) / late viral transcription / DNA replication, Okazaki fragment processing / double-stranded DNA 5'-3' DNA exonuclease activity / DNA exonuclease activity / double-stranded DNA endonuclease activity / 5'-flap endonuclease activity / 5'-3' exonuclease activity / viral DNA genome replication / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / 5'-3' DNA exonuclease activity / 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 speciesBACTERIOPHAGE T5 (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsCeska, T.A. / Sayers, J.R. / Suck, D.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2004
Title: Roles of Divalent Metal Ions in Flap Endonuclease-Substrate Interactions
Authors: Feng, M. / Patel, D. / Dervan, J. / Ceska, T.A. / Suck, D. / Haq, I. / Sayers, J.R.
History
DepositionDec 4, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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 / _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: EXODEOXYRIBONUCLEASE
B: EXODEOXYRIBONUCLEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,1154
Polymers66,9842
Non-polymers1312
Water4,017223
1
A: EXODEOXYRIBONUCLEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5572
Polymers33,4921
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: EXODEOXYRIBONUCLEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5572
Polymers33,4921
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)77.940, 77.940, 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 EXODEOXYRIBONUCLEASE / / 5'-EXONUCLEASE


Mass: 33491.867 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACTERIOPHAGE T5 (virus) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P06229, exodeoxyribonuclease (lambda-induced)
#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 223 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.05 Å3/Da / Density % sol: 65 %
Crystal growpH: 5.6 / Details: 35% AMMONIUM SULFATE, 100MM SODIUM CITRATE PH 5.6
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop / Details: Ceska, T.A., (1993) J.Mol.Biol., 233, 179.
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

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: XENTRONICS / Detector: AREA DETECTOR / Date: Nov 15, 1996
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.75→40 Å / Num. obs: 56234 / % possible obs: 84.5 % / Redundancy: 1.2 % / Rmerge(I) obs: 0.076
Reflection
*PLUS
Highest resolution: 2.75 Å / Lowest resolution: 40 Å / Num. obs: 17651 / Num. measured all: 56234 / Rmerge(I) obs: 0.076

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Processing

Software
NameVersionClassification
CNX2000refinement
XDSdata reduction
XDSdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EXN

1exn


Resolution: 2.75→25 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.313 1729 10 %RANDOM
Rwork0.235 ---
obs-17651 84.5 %-
Solvent computationSolvent model: MASK / Bsol: 66.2 Å2 / ksol: 0.4 e/Å3
Refinement stepCycle: LAST / Resolution: 2.75→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4399 0 2 223 4624
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.21
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noTopol fileParam file
X-RAY DIFFRACTION1PROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA.TOPDNA-RNA_REP.PARAM
X-RAY DIFFRACTION3WATER.TOPWATER_REP.PARAM
X-RAY DIFFRACTION4ION.TOPION.PARAM
Refinement
*PLUS
Lowest resolution: 40 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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