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- PDB-4jcv: Crystal structure of the RecOR complex in an open conformation -

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Basic information

Entry
Database: PDB / ID: 4jcv
TitleCrystal structure of the RecOR complex in an open conformation
Components
  • DNA repair protein RecO
  • Recombination protein RecRGenetic recombination
KeywordsRECOMBINATION / HOMOLOGOUS RECOMBINATION / RECFOR PATHWAY / DNA BINDING / ZINC-FINGER / DNA DAMAGE / DNA REPAIR / RECR / RECO / RECOR
Function / homology
Function and homology information


bacterial nucleoid / double-strand break repair / DNA recombination / DNA binding / metal ion binding
Similarity search - Function
Recombination protein O, zinc-binding domain / Recombination protein O, C-terminal domain / Erythroid Transcription Factor GATA-1; Chain A / Recombination protein O, C-terminal / Recombination protein O, RecO / DNA replication/recombination mediator RecO, N-terminal / Recombination protein O C terminal / Recombination protein O N terminal / RecR, C-terminal / RecR, helix-hairpin-helix ...Recombination protein O, zinc-binding domain / Recombination protein O, C-terminal domain / Erythroid Transcription Factor GATA-1; Chain A / Recombination protein O, C-terminal / Recombination protein O, RecO / DNA replication/recombination mediator RecO, N-terminal / Recombination protein O C terminal / Recombination protein O N terminal / RecR, C-terminal / RecR, helix-hairpin-helix / DNA recombination protein RecR / Recombination protein RecR, conserved site / Recombination protein RecR / RecR, TOPRIM domain / RecR, Cys4-zinc finger motif / RecR protein signature. / Toprim domain / Dna Topoisomerase Vi A Subunit; Chain: A, domain 2 / Dna Topoisomerase Vi A Subunit; Chain: A, domain 2 - #10 / ARFGAP/RecO-like zinc finger / de novo design (two linked rop proteins) / TOPRIM / Toprim domain / Other non-globular / Toprim domain profile. / TOPRIM domain / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / Nucleic acid-binding proteins / Special / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Up-down Bundle / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA repair protein RecO / Recombination protein RecR
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.34 Å
AuthorsRadzimanowski, J. / McSweeney, S. / Timmins, J.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: An 'open' structure of the RecOR complex supports ssDNA binding within the core of the complex.
Authors: Radzimanowski, J. / Dehez, F. / Round, A. / Bidon-Chanal, A. / McSweeney, S. / Timmins, J.
History
DepositionFeb 22, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _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: Recombination protein RecR
B: Recombination protein RecR
C: Recombination protein RecR
D: Recombination protein RecR
E: DNA repair protein RecO
F: DNA repair protein RecO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,79212
Polymers162,4006
Non-polymers3926
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21580 Å2
ΔGint-159 kcal/mol
Surface area54590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.130, 93.110, 92.350
Angle α, β, γ (deg.)103.60, 110.42, 106.22
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Recombination protein RecR / Genetic recombination


Mass: 26143.781 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Strain: R1 / Gene: recR, DR_0198 / Plasmid: PDEST17 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: Q9ZNA2
#2: Protein DNA repair protein RecO / / Recombination protein O


Mass: 28912.260 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Strain: R1 / Gene: recO, DR_0819 / Plasmid: PDEST17 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: Q9RW50
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn

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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: 3.07 Å3/Da / Density % sol: 59.96 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES pH 6.5, 10% dioxane, 1.6M ammonium sulphate, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.34→83.07 Å / Num. obs: 24029 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.8 %
Reflection shellResolution: 3.34→3.52 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.061 / Mean I/σ(I) obs: 8.8 / Num. unique all: 24029 / Rsym value: 0.061

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.6.0116refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VDD, 1W3S

1vdd

1w3s


Resolution: 3.34→83.07 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.903 / SU B: 73.357 / SU ML: 0.552 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R Free: 0.611 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2781 1212 5 %RANDOM
Rwork0.24016 ---
obs0.24203 22815 94.21 %-
all-24029 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 113.5 Å2
Baniso -1Baniso -2Baniso -3
1--1.53 Å22.68 Å23.19 Å2
2--3.58 Å24.7 Å2
3---3.89 Å2
Refinement stepCycle: LAST / Resolution: 3.34→83.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9156 0 6 0 9162
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0199343
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3291.99212713
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1651196
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.03822.872383
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.707151513
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3141587
X-RAY DIFFRACTIONr_chiral_restr0.0840.21473
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0227080
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.34→3.427 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 92 -
Rwork0.316 1709 -
obs--96.26 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.161-2.4630.42073.7345-0.26871.2457-0.0004-0.5687-0.1837-0.31160.21540.19880.1335-0.0495-0.2150.2024-0.10440.01840.19720.05940.173-46.322133.397222.1079
24.4038-0.83591.65361.419-0.83072.308-0.08880.05650.5255-0.2218-0.0498-0.21860.05680.13980.13860.2397-0.07060.10520.10960.04650.2232-77.02653.712110.2891
33.7197-2.0551-0.19595.62460.74262.03240.55830.8261-0.6427-0.8935-0.2820.12360.8144-0.3202-0.27630.83070.0354-0.03750.78570.16490.4636-77.163936.6008-21.352
43.27060.45372.05141.25120.29775.00180.23150.7422-0.5213-0.79690.06110.00590.23720.0625-0.29250.8998-0.0132-0.11990.2826-0.03660.9598-51.44049.0352-4.2263
54.19520.9018-0.14083.532-1.84796.549-0.0585-0.6750.09280.77050.098-0.3537-0.22280.6746-0.03950.37710.12420.04910.88280.03870.3042-54.514458.1699-24.7346
64.04670.7133-0.62589.6283-1.02972.171-0.3372-0.62111.06970.56840.12210.5391-0.7047-0.55890.21520.45510.125-0.18550.4906-0.28190.9437-71.7872-0.985417.4729
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 197
2X-RAY DIFFRACTION2B2 - 197
3X-RAY DIFFRACTION3C9 - 199
4X-RAY DIFFRACTION4D4 - 199
5X-RAY DIFFRACTION5E3 - 226
6X-RAY DIFFRACTION6F5 - 227

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