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- PDB-1u5k: Recombinational repair protein RecO -

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Basic information

Entry
Database: PDB / ID: 1u5k
TitleRecombinational repair protein RecO
Componentshypothetical protein
KeywordsRECOMBINATION / REPLICATION / OBD-fold / Zn-binding
Function / homology
Function and homology information


bacterial nucleoid / double-strand break repair / DNA recombination / 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, RecO / DNA replication/recombination mediator RecO, N-terminal / Recombination protein O, C-terminal / Recombination protein O C terminal / Recombination protein O N terminal / ARFGAP/RecO-like zinc finger / de novo design (two linked rop proteins) ...Recombination protein O, zinc-binding domain / Recombination protein O, C-terminal domain / Erythroid Transcription Factor GATA-1; Chain A / Recombination protein O, RecO / DNA replication/recombination mediator RecO, N-terminal / Recombination protein O, C-terminal / Recombination protein O C terminal / Recombination protein O N terminal / ARFGAP/RecO-like zinc finger / de novo design (two linked rop proteins) / Other non-globular / Nucleic acid-binding proteins / Special / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Up-down Bundle / Beta Barrel / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
DNA repair protein RecO
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsMakharashvili, N. / Koroleva, O. / Bera, S. / Grandgenett, D.P. / Korolev, S.
CitationJournal: STRUCTURE / Year: 2004
Title: A Novel Structure of DNA Repair Protein RecO from Deinococcus radiodurans
Authors: Makharashvili, N. / Koroleva, O. / Bera, S. / Grandgenett, D.P. / Korolev, S.
History
DepositionJul 27, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: hypothetical protein
B: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8844
Polymers52,7532
Non-polymers1312
Water4,918273
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)134.967, 52.240, 100.683
Angle α, β, γ (deg.)90.00, 107.09, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein hypothetical protein


Mass: 26376.443 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Strain: R1 / Gene: DR0819 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RW50
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 3.22 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG4000, MgCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-BM11.28309
SYNCHROTRONAPS 19-BM21.28255
Detector
TypeIDDetectorDate
SBC-11CCDMar 5, 2004
SBC-12CCDMar 5, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.283091
21.282551
ReflectionResolution: 2→50 Å / Num. obs: 45542 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 20
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.553 / Mean I/σ(I) obs: 2.2 / % possible all: 94.6

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
SBC-Collectdata collection
SCALEPACKdata scaling
SHARPphasing
ARP/wARPmodel building
Omodel building
RefinementMethod to determine structure: MAD / Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.676 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.13
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21345 2299 5 %RANDOM
Rwork0.19799 ---
all0.19879 ---
obs0.19879 43223 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.317 Å2
Baniso -1Baniso -2Baniso -3
1-1.04 Å20 Å20.49 Å2
2---0.95 Å20 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3586 0 2 273 3861
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0213678
X-RAY DIFFRACTIONr_bond_other_d0.0060.023462
X-RAY DIFFRACTIONr_angle_refined_deg1.7441.9595012
X-RAY DIFFRACTIONr_angle_other_deg0.94437997
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1855469
X-RAY DIFFRACTIONr_chiral_restr0.1180.2564
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024114
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02764
X-RAY DIFFRACTIONr_nbd_refined0.2370.2787
X-RAY DIFFRACTIONr_nbd_other0.2660.23896
X-RAY DIFFRACTIONr_nbtor_other0.0890.22101
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2206
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3320.281
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1930.211
X-RAY DIFFRACTIONr_mcbond_it1.1181.52371
X-RAY DIFFRACTIONr_mcangle_it2.04923795
X-RAY DIFFRACTIONr_scbond_it3.21831307
X-RAY DIFFRACTIONr_scangle_it5.2954.51217
LS refinement shellResolution: 1.999→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.267 169
Rwork0.263 3085

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