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- PDB-6m9k: Crystal structure of lambda exonuclease in complex with the Red b... -

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Basic information

Entry
Database: PDB / ID: 6m9k
TitleCrystal structure of lambda exonuclease in complex with the Red beta C-terminal domain
Components
  • Exonuclease
  • Recombination protein bet
KeywordsHYDROLASE / protein-protein complex
Function / homology
Function and homology information


exodeoxyribonuclease (lambda-induced) / double-stranded DNA 5'-3' DNA exonuclease activity / DNA recombination / DNA binding / metal ion binding
Similarity search - Function
Bacteriophage lambda, Recombination protein bet / YqaJ viral recombinase / : / YqaJ-like viral recombinase domain / RecT family / RecT family / Lambda Exonuclease; Chain A - #10 / Lambda Exonuclease; Chain A / PD-(D/E)XK endonuclease-like domain superfamily / Restriction endonuclease type II-like ...Bacteriophage lambda, Recombination protein bet / YqaJ viral recombinase / : / YqaJ-like viral recombinase domain / RecT family / RecT family / 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
Exonuclease / Recombination protein bet
Similarity search - Component
Biological speciesEscherichia phage lambda (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
Model detailsfull-length lambda exonuclease trimer with three copies of the Red beta C-terminal domain residues 183-261
AuthorsBell, C.E. / Caldwell, B.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1616105 United States
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Crystal structure of the Red beta C-terminal domain in complex with lambda Exonuclease reveals an unexpected homology with lambda Orf and an interaction with Escherichia coli single stranded DNA binding protein.
Authors: Caldwell, B.J. / Zakharova, E. / Filsinger, G.T. / Wannier, T.M. / Hempfling, J.P. / Chun-Der, L. / Pei, D. / Church, G.M. / Bell, C.E.
History
DepositionAug 23, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 2, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 13, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Exonuclease
B: Exonuclease
C: Exonuclease
D: Recombination protein bet
E: Recombination protein bet
F: Recombination protein bet
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,93022
Polymers100,3936
Non-polymers1,53716
Water10,863603
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10900 Å2
ΔGint-241 kcal/mol
Surface area41230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.522, 122.522, 147.858
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Exonuclease


Mass: 25940.586 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: no purification tag / Source: (gene. exp.) Escherichia phage lambda (virus) / Gene: exo, red-alpha, redX / Plasmid: pET28B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(AI)
References: UniProt: P03697, exodeoxyribonuclease (lambda-induced)
#2: Protein Recombination protein bet


Mass: 7523.592 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: N-terminal 6XHis tag cleaved off by thrombin / Source: (gene. exp.) Escherichia phage lambda (virus) / Gene: bet, betA, red-beta, redB / Plasmid: pET14B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(AI) / References: UniProt: P03698
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 603 / 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: 3.19 Å3/Da / Density % sol: 61.46 % / Mosaicity: 0.69 °
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8 / Details: PEG3350, LISO4, BIS-TRIS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS3 R 200K-A / Detector: PIXEL / Date: Mar 16, 2018 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→106.11 Å / Num. obs: 57486 / % possible obs: 99.7 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.071 / Rrim(I) all: 0.149 / Χ2: 1.746 / Net I/σ(I): 6.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.342.30.5828220.4610.460.7471.1799.1
2.34-2.382.40.54428100.5050.4210.6941.1799.4
2.38-2.432.40.52228580.5090.4040.6661.1999.4
2.43-2.482.50.47828190.5820.3630.6051.15799.7
2.48-2.532.60.43628580.6720.3260.5491.19599.6
2.53-2.592.60.428290.730.2960.5021.18299.6
2.59-2.662.70.37528360.7870.2710.4661.1999.6
2.66-2.732.80.33728750.8050.2410.4171.15899.6
2.73-2.8130.31628260.8480.2190.3871.20699.7
2.81-2.93.10.27628450.8990.1840.3341.266100
2.9-33.40.25328880.9150.160.3011.322100
3-3.123.60.21728520.940.1310.2551.446100
3.12-3.263.80.17528730.9650.1020.2031.665100
3.26-3.444.10.15228870.9710.0820.1741.976100
3.44-3.654.60.13328610.9830.0670.152.09100
3.65-3.935.20.11929040.9880.0550.1312.436100
3.93-4.336.10.10429070.9910.0440.1132.375100
4.33-4.9570.08829230.9950.0350.0952.117100
4.95-6.246.80.08429480.9950.0340.0911.72599.9
6.24-506.10.04930650.9980.0210.0531.89299.3

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AVQ

1avq


Resolution: 2.3→106.11 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.898 / SU B: 8.119 / SU ML: 0.184 / SU R Cruickshank DPI: 0.2547 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.255 / ESU R Free: 0.221 / Details: REFMAC5, NO NCS RESTRAINTS
RfactorNum. reflection% reflectionSelection details
Rfree0.2535 2782 4.8 %RANDOM
Rwork0.1953 ---
obs0.1982 54662 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 106.5 Å2 / Biso mean: 31.808 Å2 / Biso min: 10.07 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20.07 Å20 Å2
2--0.14 Å20 Å2
3----0.45 Å2
Refinement stepCycle: final / Resolution: 2.3→106.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6890 0 80 603 7573
Biso mean--76.15 31.44 -
Num. residues----873
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0197103
X-RAY DIFFRACTIONr_bond_other_d0.0020.026599
X-RAY DIFFRACTIONr_angle_refined_deg1.2711.969625
X-RAY DIFFRACTIONr_angle_other_deg0.938315181
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8045867
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.96224.281327
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.196151209
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1341543
X-RAY DIFFRACTIONr_chiral_restr0.0730.21059
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027956
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021607
LS refinement shellResolution: 2.298→2.357 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 227 -
Rwork0.297 3904 -
all-4131 -
obs--98.12 %

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