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- PDB-6lrd: Structure of RecJ complexed with a 5'-P-dSpacer-modified ssDNA -

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Basic information

Entry
Database: PDB / ID: 6lrd
TitleStructure of RecJ complexed with a 5'-P-dSpacer-modified ssDNA
Components
  • ASP-LEU-PRO-PHE
  • DNA (5'-D(P*(3DR)P*TP*TP*TP*TP*T)-3')
  • Single-stranded-DNA-specific exonuclease
KeywordsDNA BINDING PROTEIN/DNA / nuclease / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


5'-3' exonuclease activity / DNA recombination / nucleic acid binding / DNA repair / metal ion binding
Similarity search - Function
Bacterial RecJ exonuclease / : / RecJ C-terminal domain, Deinococci / RecJ, OB domain / RecJ OB domain / DDH domain / DHH family / DHH phosphoesterase superfamily / DHHA1 domain / DHHA1 domain
Similarity search - Domain/homology
: / DNA / Single-stranded-DNA-specific exonuclease RecJ
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.90133495575 Å
AuthorsCheng, K. / Hua, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31670065 China
National Natural Science Foundation of China (NSFC)31870051 China
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Participation of RecJ in the base excision repair pathway of Deinococcus radiodurans.
Authors: Cheng, K. / Xu, Y. / Chen, X. / Lu, H. / He, Y. / Wang, L. / Hua, Y.
History
DepositionJan 16, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 7, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 29, 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: Single-stranded-DNA-specific exonuclease
C: DNA (5'-D(P*(3DR)P*TP*TP*TP*TP*T)-3')
B: ASP-LEU-PRO-PHE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,6729
Polymers78,1783
Non-polymers4946
Water8,125451
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-84 kcal/mol
Surface area29710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.140, 106.140, 164.560
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

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Protein / DNA chain / Protein/peptide , 3 types, 3 molecules ACB

#1: Protein Single-stranded-DNA-specific exonuclease


Mass: 76031.539 Da / Num. of mol.: 1 / Mutation: H160A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Gene: recJ / Production host: Escherichia coli (E. coli) / References: UniProt: D0EM60
#2: DNA chain DNA (5'-D(P*(3DR)P*TP*TP*TP*TP*T)-3')


Mass: 1656.102 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein/peptide ASP-LEU-PRO-PHE


Mass: 490.549 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 457 molecules

#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 451 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.42 Å3/Da / Density % sol: 64.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: MES, MnCl2, Li2SO4

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 83333 / % possible obs: 98.3 % / Redundancy: 5 % / Biso Wilson estimate: 35.4640529398 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 19
Reflection shellResolution: 1.9→1.95 Å / Rmerge(I) obs: 0.599

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
Cootmodel building
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5f56

5f56


Resolution: 1.90133495575→29.3506116493 Å / SU ML: 0.223697505373 / Cross valid method: NONE / σ(F): 1.3378883985 / Phase error: 24.9139955613
RfactorNum. reflection% reflection
Rfree0.233801995079 4131 4.95721982888 %
Rwork0.208480144714 --
obs0.209731808078 83333 98.2909108065 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 45.1754609173 Å2
Refinement stepCycle: LAST / Resolution: 1.90133495575→29.3506116493 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5313 112 22 451 5898
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007294934567425604
X-RAY DIFFRACTIONf_angle_d0.9468719314347684
X-RAY DIFFRACTIONf_chiral_restr0.0498713247204869
X-RAY DIFFRACTIONf_plane_restr0.005796637387681003
X-RAY DIFFRACTIONf_dihedral_angle_d16.43955904163356
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9014-1.92290.3574943618911200.3405650206912530X-RAY DIFFRACTION94.4404846757
1.9229-1.94560.3284286047861590.3115700615472589X-RAY DIFFRACTION99.2774566474
1.9456-1.96930.3178101202521350.2974269641172650X-RAY DIFFRACTION99.4642857143
1.9693-1.99420.3191280495341380.2837227184062651X-RAY DIFFRACTION99.6783416726
1.9942-2.02040.283005653741630.2762585138472643X-RAY DIFFRACTION99.4330262225
2.0204-2.04810.2686693457921480.2609756756452597X-RAY DIFFRACTION99.3845039826
2.0481-2.07740.3098653876551600.2576290145292628X-RAY DIFFRACTION99.6782266714
2.0774-2.10840.3049478159331590.2501174522612653X-RAY DIFFRACTION99.6456413891
2.1084-2.14130.2735611641631340.2512849588742637X-RAY DIFFRACTION99.7480201584
2.1413-2.17640.2805350839281530.2363100958672635X-RAY DIFFRACTION99.7138769671
2.1764-2.21390.2726263057051440.2366522324042676X-RAY DIFFRACTION99.7523876901
2.2139-2.25410.3084057831561380.2249821831692649X-RAY DIFFRACTION99.8209169054
2.2541-2.29750.246217086671280.2226824368522670X-RAY DIFFRACTION99.7860199715
2.2975-2.34440.2259376048641250.219980230512642X-RAY DIFFRACTION99.9277717588
2.3444-2.39530.2525099210271330.2124949411052698X-RAY DIFFRACTION99.8236953456
2.3953-2.4510.2410844948191360.2180960266382681X-RAY DIFFRACTION99.8582063098
2.451-2.51230.2602273402321060.2223428676032701X-RAY DIFFRACTION99.8221906117
2.5123-2.58020.2526383148291320.2212210332312667X-RAY DIFFRACTION99.8929336188
2.5802-2.6560.2416423563751260.219817176562712X-RAY DIFFRACTION99.8592540464
2.656-2.74170.2415841351471490.2261657843212641X-RAY DIFFRACTION99.7854077253
2.7417-2.83960.2762259536141580.2187130053562663X-RAY DIFFRACTION99.6467679265
2.8396-2.95320.2072054205521400.2057564645462676X-RAY DIFFRACTION99.716713881
2.9532-3.08750.2639446453621230.220551159662696X-RAY DIFFRACTION99.5058242146
3.0875-3.25010.2594751804811260.2157365241072707X-RAY DIFFRACTION99.6482588815
3.2501-3.45340.2357458010281470.1989143735092659X-RAY DIFFRACTION99.4330262225
3.4534-3.71950.2179683593881460.1877385044552693X-RAY DIFFRACTION99.1270949721
3.7195-4.0930.1937302312461410.1727586537852682X-RAY DIFFRACTION98.4652947332
4.093-4.68320.1757863193051380.1622570714142659X-RAY DIFFRACTION97.1180555556
4.6832-5.89240.198095836381340.1903764224822688X-RAY DIFFRACTION96.4456596036
5.8924-29.35009790.239144095266920.2176534353392129X-RAY DIFFRACTION73.1554677207

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