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- PDB-4ad8: Crystal structure of a deletion mutant of Deinococcus radiodurans RecN -

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Basic information

Entry
Database: PDB / ID: 4ad8
TitleCrystal structure of a deletion mutant of Deinococcus radiodurans RecN
ComponentsDNA REPAIR PROTEIN RECN
KeywordsDNA BINDING PROTEIN / DNA REPAIR / ATPASE DOMAIN
Function / homology
Function and homology information


bacterial nucleoid / SOS response / DNA recombination / DNA repair / ATP binding / identical protein binding
Similarity search - Function
DNA recombination/repair protein RecN / RecF/RecN/SMC, N-terminal / RecF/RecN/SMC N terminal domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA repair protein RecN
Similarity search - Component
Biological speciesDEINOCOCCUS RADIODURANS (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.998 Å
AuthorsPellegrino, S. / Radzimanowski, J. / de Sanctis, D. / McSweeney, S. / Timmins, J.
CitationJournal: Structure / Year: 2012
Title: Structural and Functional Characterization of an Smc-Like Protein Recn: New Insights Into Double-Strand Break Repair.
Authors: Pellegrino, S. / Radzimanowski, J. / De Sanctis, D. / Erba, E.B. / Mcsweeney, S. / Timmins, J.
History
DepositionDec 22, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2012Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA REPAIR PROTEIN RECN


Theoretical massNumber of molelcules
Total (without water)55,1551
Polymers55,1551
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.205, 62.487, 145.526
Angle α, β, γ (deg.)90.00, 98.39, 90.00
Int Tables number5
Space group name H-MI121

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Components

#1: Protein DNA REPAIR PROTEIN RECN / RECOMBINATION PROTEIN N / RECN


Mass: 55154.637 Da / Num. of mol.: 1
Fragment: HEAD AND PARTIAL COILED-COIL DOMAINS, RESIDUES 1-237,305-564
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DEINOCOCCUS RADIODURANS (radioresistant)
Strain: R1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): STAR / References: UniProt: Q9WXF2, EC: 3.6.1.3
Sequence detailsLINKER PEPTIDE ESSKHPTSLVPRGS

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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: 3.12 Å3/Da / Density % sol: 60.6 % / Description: NONE
Crystal growDetails: 0.1 M SODIUM CACODYLATE TRIHYDRATE PH 6.5, 0.2 M MAGNESIUM ACETATE TETRAHYDRATE, 10% W/V PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 4→47 Å / Num. obs: 5430 / % possible obs: 97.5 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 87.28 Å2 / Rmerge(I) obs: 0.28 / Net I/σ(I): 3.8
Reflection shellResolution: 4→4.21 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 1.5 / % possible all: 93.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4ABY

4aby


Resolution: 3.998→47.031 Å / SU ML: 1.39 / σ(F): 1.38 / Phase error: 38.56 / Stereochemistry target values: ML
Details: THE B-FACTOR VALUES HAVE BEEN SET TO THE ESTIMATE FROM THE WILSON PLOT DETERMINED BY XDS AND NOT FURTHER REFINED. THIS IS OWING TO THE LOW RESOLUTION OF THE DATA.
RfactorNum. reflection% reflection
Rfree0.347 246 4.5 %
Rwork0.3251 --
obs0.326 5413 96.89 %
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 10.671 Å2 / ksol: 0.285 e/Å3
Displacement parametersBiso mean: 70 Å2
Baniso -1Baniso -2Baniso -3
1-19.6992 Å20 Å2-63.1796 Å2
2--30.6727 Å20 Å2
3---52.4164 Å2
Refinement stepCycle: LAST / Resolution: 3.998→47.031 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3416 0 0 0 3416
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033458
X-RAY DIFFRACTIONf_angle_d0.6944675
X-RAY DIFFRACTIONf_dihedral_angle_d11.9071279
X-RAY DIFFRACTIONf_chiral_restr0.04542
X-RAY DIFFRACTIONf_plane_restr0.003621
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.9976-5.03560.37951330.35512538X-RAY DIFFRACTION97
5.0356-47.03470.31911130.30382629X-RAY DIFFRACTION97

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