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- PDB-3q8d: E. coli RecO complex with SSB C-terminus -

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Basic information

Entry
Database: PDB / ID: 3q8d
TitleE. coli RecO complex with SSB C-terminus
Components
  • DNA repair protein recO
  • Single-stranded DNA-binding protein
KeywordsDNA BINDING PROTEIN / DNA-binding protein / OB-fold / recombination initation / recombination initiation / SSB / DNA / RecR
Function / homology
Function and homology information


single-stranded DNA-binding protein complex / bacterial nucleoid / nucleoid / replisome / recombinational repair / positive regulation of catalytic activity / SOS response / mismatch repair / enzyme activator activity / response to radiation ...single-stranded DNA-binding protein complex / bacterial nucleoid / nucleoid / replisome / recombinational repair / positive regulation of catalytic activity / SOS response / mismatch repair / enzyme activator activity / response to radiation / DNA-templated DNA replication / double-strand break repair / single-stranded DNA binding / DNA recombination / identical protein binding / cytosol
Similarity search - Function
Recombination protein O, C-terminal domain / Recombination protein O, RecO / DNA replication/recombination mediator RecO, N-terminal / Recombination protein O C terminal / Recombination protein O N terminal / Single-stranded DNA-binding protein / ARFGAP/RecO-like zinc finger / Single-strand binding protein family / Single-strand binding (SSB) domain profile. / Primosome PriB/single-strand DNA-binding ...Recombination protein O, C-terminal domain / Recombination protein O, RecO / DNA replication/recombination mediator RecO, N-terminal / Recombination protein O C terminal / Recombination protein O N terminal / Single-stranded DNA-binding protein / ARFGAP/RecO-like zinc finger / Single-strand binding protein family / Single-strand binding (SSB) domain profile. / Primosome PriB/single-strand DNA-binding / de novo design (two linked rop proteins) / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Up-down Bundle / Beta Barrel / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
D-MALATE / : / : / DNA repair protein RecO / Single-stranded DNA-binding protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsKoroleva, O. / Ryzhikov, M. / Korolev, S.
CitationJournal: Nucleic Acids Res. / Year: 2011
Title: Mechanism of RecO recruitment to DNA by single-stranded DNA binding protein.
Authors: Ryzhikov, M. / Koroleva, O. / Postnov, D. / Tran, A. / Korolev, S.
History
DepositionJan 6, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 29, 2012Group: Database references
Revision 1.3Jan 30, 2013Group: Non-polymer description
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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: DNA repair protein recO
B: DNA repair protein recO
E: Single-stranded DNA-binding protein
F: Single-stranded DNA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2597
Polymers57,4184
Non-polymers8413
Water3,711206
1
A: DNA repair protein recO
E: Single-stranded DNA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9354
Polymers28,7092
Non-polymers2262
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA repair protein recO
F: Single-stranded DNA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3243
Polymers28,7092
Non-polymers6151
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.199, 118.569, 145.119
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABEF

#1: Protein DNA repair protein recO / Recombination protein O


Mass: 27431.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: recO / Production host: Escherichia coli (E. coli) / References: UniProt: D5CXR1, UniProt: P0A7H3*PLUS
#2: Protein/peptide Single-stranded DNA-binding protein


Mass: 1277.356 Da / Num. of mol.: 2 / Fragment: unp residues 170-178
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ssb / Production host: Escherichia coli (E. coli) / References: UniProt: D5D6S3, UniProt: P0AGE0*PLUS

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Non-polymers , 4 types, 209 molecules

#3: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CPS / 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE / CHAPS


Mass: 614.877 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H58N2O7S / Comment: detergent*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.75 Å3/Da / Density % sol: 67.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 23-ID-D10.97953
SYNCHROTRONAPS 23-ID-D20.97953
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 17, 2010
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.97953 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 38294 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.064
Reflection shellResolution: 2.3→2.34 Å / Rmerge(I) obs: 0.653 / Mean I/σ(I) obs: 1.8 / Num. unique all: 1662 / % possible all: 87.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→40 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.924 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23406 1867 5.2 %RANDOM
Rwork0.19469 ---
obs0.19678 33949 93.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.315 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å20 Å2
2--0.12 Å20 Å2
3----0.46 Å2
Refinement stepCycle: LAST / Resolution: 2.3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3725 0 57 206 3988
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223871
X-RAY DIFFRACTIONr_angle_refined_deg1.0051.9965229
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.5585466
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.00521.243169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.15315656
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1321544
X-RAY DIFFRACTIONr_chiral_restr0.0850.2578
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.0212896
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_it2.0771.52331
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.73723730
X-RAY DIFFRACTIONr_scbond_it5.33931540
X-RAY DIFFRACTIONr_scangle_it8.2574.51499
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 108 -
Rwork0.33 1919 -
obs--80.69 %

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