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- PDB-2v1c: Crystal structure and mutational study of RecOR provide insight i... -

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Basic information

Entry
Database: PDB / ID: 2v1c
TitleCrystal structure and mutational study of RecOR provide insight into its role in DNA repair
Components
  • HYPOTHETICAL PROTEIN
  • RECOMBINATION PROTEIN RECRGenetic recombination
KeywordsRECOMBINATION / HOMOLOGOUS RECOMBINATION / RECFOR PATHWAY / DNA RECOMBINATION / DNA BINDING / ZINC-FINGER / METAL-BINDING / RECOR COMPLEX / HYPOTHETICAL PROTEIN / DEINOCOCCUS RADIODURANS / RECR / ZINC / RECO / DNA DAMAGE / DNA REPAIR
Function / homology
Function and homology information


bacterial nucleoid / double-strand break repair / DNA recombination / DNA binding / metal ion binding
Similarity search - Function
RecR Domain 1 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #240 / Recombination protein O, zinc-binding domain / Recombination protein O, C-terminal domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #80 / 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 ...RecR Domain 1 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #240 / Recombination protein O, zinc-binding domain / Recombination protein O, C-terminal domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #80 / 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 / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Toprim domain / Other non-globular / Toprim domain profile. / TOPRIM domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / Helicase, Ruva Protein; domain 3 / Nucleic acid-binding proteins / Helix non-globular / Special / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Up-down Bundle / Beta Barrel / 2-Layer Sandwich / Orthogonal Bundle / 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: 3.8 Å
AuthorsTimmins, J. / Leiros, I. / McSweeney, S.
CitationJournal: Embo J. / Year: 2007
Title: Crystal Structure and Mutational Study of Recor Provide Insight Into its Mode of DNA Binding.
Authors: Timmins, J. / Leiros, I. / Mcsweeney, S.
History
DepositionMay 23, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / 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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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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: HYPOTHETICAL PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,0776
Polymers73,8813
Non-polymers1963
Water0
1
A: RECOMBINATION PROTEIN RECR
B: RECOMBINATION PROTEIN RECR
C: HYPOTHETICAL PROTEIN
hetero molecules

A: RECOMBINATION PROTEIN RECR
B: RECOMBINATION PROTEIN RECR
C: HYPOTHETICAL PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,15412
Polymers147,7626
Non-polymers3926
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
MethodPQS
Unit cell
Length a, b, c (Å)144.000, 83.200, 66.600
Angle α, β, γ (deg.)90.00, 106.90, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein RECOMBINATION PROTEIN RECR / Genetic recombination / RECR


Mass: 23752.182 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: Q9ZNA2
#2: Protein HYPOTHETICAL PROTEIN / / RECO


Mass: 26376.443 Da / Num. of mol.: 1
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
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / 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: 2.6 Å3/Da / Density % sol: 52.1 %
Crystal growDetails: 0.1 M MES PH 6.5, 10% DIOXANE, 1.6 M AMMONIUM SULPHATE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 26, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 3.8→45 Å / Num. obs: 7194 / % possible obs: 95.9 % / Redundancy: 3.1 % / Biso Wilson estimate: 96 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 6.5
Reflection shellResolution: 3.8→4 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 1.4 / % possible all: 95.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1VDD,1W3S

1vdd

1w3s


Resolution: 3.8→71.25 Å / Cor.coef. Fo:Fc: 0.644 / Cor.coef. Fo:Fc free: 0.667 / SU ML: 3.138 / Cross valid method: THROUGHOUT / ESU R: 1.508 / ESU R Free: 1.456 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THIS MODEL REPRESENTS A RIGID-BODY REFINEMENT WHERE EACH PROTEIN MONOMER WAS TREATED AS ONE RIGID BODY, FOLLOWED BY A SINGLE ROUND OF ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THIS MODEL REPRESENTS A RIGID-BODY REFINEMENT WHERE EACH PROTEIN MONOMER WAS TREATED AS ONE RIGID BODY, FOLLOWED BY A SINGLE ROUND OF MANUAL REMODELLING WITH APPROXIMATIVE FITTING OF SIDECHAINS. THE LIMITED NUMBER OF OBSERVATIONS PRECLUDED POSITIONAL REFINEMENT OF INDIVIDUAL ATOMS. RESIDUES A1, A200-A220, B1, B200-B220, C1-C2, C237-C244 ARE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.443 329 4.6 %RANDOM
Rwork0.459 ---
obs0.458 6850 95.3 %-
Displacement parametersBiso mean: 96 Å2
Baniso -1Baniso -2Baniso -3
1--7.26 Å20 Å2-1.84 Å2
2--9.04 Å20 Å2
3----2.85 Å2
Refinement stepCycle: LAST / Resolution: 3.8→71.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4778 0 3 0 4781
LS refinement shellResolution: 3.8→3.9 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.487 24
Rwork0.46 457

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