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- PDB-1w3s: The crystal structure of RecO from Deinococcus radiodurans. -

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Basic information

Entry
Database: PDB / ID: 1w3s
TitleThe crystal structure of RecO from Deinococcus radiodurans.
ComponentsHYPOTHETICAL PROTEIN DR0819
KeywordsDNA REPAIR / SAD / CYS4 ZINC FINGER / OB-FOLD / RECO
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 / OTHER / Resolution: 2.4 Å
AuthorsLeiros, I. / Timmins, J. / Hall, D.R. / Leonard, G.A. / McSweeney, S.M.
CitationJournal: Embo J. / Year: 2005
Title: Crystal Structure and DNA-Binding Analysis of Reco from Deinococcus Radiodurans
Authors: Leiros, I. / Timmins, J. / Hall, D.R. / Mcsweeney, S.M.
History
DepositionJul 18, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 23, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" AND "BA" IN EACH CHAIN ON SHEET ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" AND "BA" IN EACH CHAIN ON SHEET RECORDS BELOW ARE ACTUALLY 6-STRANDED BARRELS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HYPOTHETICAL PROTEIN DR0819
B: HYPOTHETICAL PROTEIN DR0819
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8844
Polymers52,7532
Non-polymers1312
Water41423
1
A: HYPOTHETICAL PROTEIN DR0819
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4422
Polymers26,3761
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: HYPOTHETICAL PROTEIN DR0819
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4422
Polymers26,3761
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)134.429, 52.351, 101.085
Angle α, β, γ (deg.)90.00, 106.32, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein HYPOTHETICAL PROTEIN DR0819 / RECO


Mass: 26376.443 Da / Num. of mol.: 2
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(DE3) / 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.: 23 / 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: 2.9 Å3/Da / Density % sol: 58 %
Description: THE STRUCTURE WAS SOLVED BY THE SAD METHOD ON A DATA SET COLLECTED AT THE ZINC ABSORPTION EDGE.
Crystal growpH: 8.5
Details: 0.2 M CALCIUM ACETATE, 8% (W/V) PEG 20000, 8% (W/V) PEG 550 MONOMETHYL ETHER (MME), 0.1 M TRIS/HCL PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.4→48.6 Å / Num. obs: 26328 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.6
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 1.4 / % possible all: 99.7

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
SOLVEphasing
SHARPphasing
REFMAC5.2.0003refinement
RefinementMethod to determine structure: OTHER / Resolution: 2.4→95.35 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.921 / SU B: 9.753 / SU ML: 0.219 / Cross valid method: THROUGHOUT / ESU R: 0.317 / ESU R Free: 0.247 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.267 1332 5.1 %RANDOM
Rwork0.225 ---
obs0.227 24995 98.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 53.75 Å2
Baniso -1Baniso -2Baniso -3
1-2.34 Å20 Å22.18 Å2
2---2.66 Å20 Å2
3---1.55 Å2
Refinement stepCycle: LAST / Resolution: 2.4→95.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3532 0 2 23 3557
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223624
X-RAY DIFFRACTIONr_bond_other_d0.0010.023393
X-RAY DIFFRACTIONr_angle_refined_deg1.3241.9434939
X-RAY DIFFRACTIONr_angle_other_deg0.84937844
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.035457
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.73122.208154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.79415553
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.671535
X-RAY DIFFRACTIONr_chiral_restr0.0760.2552
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024050
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02751
X-RAY DIFFRACTIONr_nbd_refined0.2110.2715
X-RAY DIFFRACTIONr_nbd_other0.1880.23278
X-RAY DIFFRACTIONr_nbtor_refined0.1750.21701
X-RAY DIFFRACTIONr_nbtor_other0.0890.22084
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.262
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1340.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2460.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9451.52942
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.01923709
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.13231482
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.7854.51230
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.36 79
Rwork0.329 1873

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