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- PDB-1avq: TOROIDAL STRUCTURE OF LAMBDA EXONUCLEASE DETERMINED AT 2.4 ANGSTROMS -

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Basic information

Entry
Database: PDB / ID: 1avq
TitleTOROIDAL STRUCTURE OF LAMBDA EXONUCLEASE DETERMINED AT 2.4 ANGSTROMS
ComponentsLAMBDA EXONUCLEASEExodeoxyribonuclease (lambda-induced)
KeywordsDEOXYRIBONUCLEASE / DNA RECOMBINATION AND REPAIR / 5'-3' EXONUCLEASE
Function / homology
Function and homology information


exodeoxyribonuclease (lambda-induced) / exonuclease activity / metal ion binding
Similarity search - Function
YqaJ viral recombinase / YqaJ-like viral recombinase domain / Lambda Exonuclease; Chain A - #10 / Lambda Exonuclease; Chain A / PD-(D/E)XK endonuclease-like domain superfamily / Restriction endonuclease type II-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / PHOSPHATE ION / Exonuclease
Similarity search - Component
Biological speciesEnterobacteria phage lambda (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR WITH ANOMALOUS DISPERSION / Resolution: 2.4 Å
AuthorsKovall, R.A. / Matthews, B.W.
CitationJournal: Science / Year: 1997
Title: Toroidal structure of lambda-exonuclease.
Authors: Kovall, R. / Matthews, B.W.
History
DepositionSep 18, 1997Processing site: BNL
Revision 1.0Mar 18, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software / Item: _software.name / _software.version
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: LAMBDA EXONUCLEASE
B: LAMBDA EXONUCLEASE
C: LAMBDA EXONUCLEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,01910
Polymers78,4973
Non-polymers5217
Water7,494416
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-53 kcal/mol
Surface area33560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.700, 156.700, 131.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-338-

HOH

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Components

#1: Protein LAMBDA EXONUCLEASE / Exodeoxyribonuclease (lambda-induced) / RED ALPHA


Mass: 26165.809 Da / Num. of mol.: 3 / Mutation: 20 AMINO ACID N-TERMINAL HIS-TAG
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage lambda (virus) / Genus: Lambda-like viruses / Cell line: BL21 / Plasmid: PET-28(A+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS
References: UniProt: P03697, exodeoxyribonuclease (lambda-induced)
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 416 / 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: 4.8 Å3/Da / Density % sol: 74 %
Crystal growTemperature: 277 K / pH: 4.7
Details: PROTEIN WAS CRYSTALLIZED FROM 1.2 M NH2SO4, 0.2 M NACL 0.1 M NAACETATE PH 4.7, AT 4 DEGREES CELSIUS., temperature 277K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.2 Mammonium salfate11
20.2 M11NaCl
30.1 Msodium acetate11

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.908
DetectorDetector: IMAGE PLATE / Date: Jan 1, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.908 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 62855 / % possible obs: 97 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 27.9 Å2 / Rsym value: 0.055 / Net I/σ(I): 11.9
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 4.7 / Rsym value: 0.251 / % possible all: 94.3
Reflection
*PLUS
Num. measured all: 291671 / Rmerge(I) obs: 0.055

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Processing

Software
NameVersionClassification
TNT5Erefinement
XTALVIEWrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR WITH ANOMALOUS DISPERSION
Resolution: 2.4→30 Å / Isotropic thermal model: TNT BCORREL / σ(F): 0 / Stereochemistry target values: TNT PROTGEO / Details: ANISOTROPIC SCALE FACTORS: B11 B22=7.26 B33=-14.53
RfactorNum. reflection% reflection
Rwork0.198 --
all-62855 -
obs-62855 97 %
Solvent computationSolvent model: TNT SOLVENT MODEL / Bsol: 235 Å2 / ksol: 0.922 e/Å3
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5486 0 31 416 5933
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01756471
X-RAY DIFFRACTIONt_angle_deg2.675981.8
X-RAY DIFFRACTIONt_dihedral_angle_d17.9533210
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0191441.1
X-RAY DIFFRACTIONt_gen_planes0.0188154.8
X-RAY DIFFRACTIONt_it5.8556351.2
X-RAY DIFFRACTIONt_nbd0.0278810
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg17.950
X-RAY DIFFRACTIONt_planar_d0.0191.1
X-RAY DIFFRACTIONt_plane_restr0.0184.8

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