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- PDB-3vdu: Structure of recombination mediator protein RecRK21G mutant -

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Basic information

Entry
Database: PDB / ID: 3vdu
TitleStructure of recombination mediator protein RecRK21G mutant
ComponentsRecombination protein recRGenetic recombination
KeywordsRECOMBINATION / Zinc Finger / DNA repair / DNA binding
Function / homology
Function and homology information


DNA recombination / DNA repair / DNA binding / metal ion binding
Similarity search - Function
RecR Domain 1 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #240 / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #80 / 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 Domain 1 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #240 / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #80 / 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 / Helix-hairpin-helix motif / TOPRIM / Wheat Germ Agglutinin (Isolectin 2); domain 1 / 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 / Helix non-globular / Special / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Recombination protein RecR
Similarity search - Component
Biological speciesThermoanaerobacter tengcongensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsTang, Q. / Yan, X.X. / Liang, D.C.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: RecOR complex including RecR N-N dimer and RecO monomer displays a high affinity for ssDNA
Authors: Tang, Q. / Gao, P. / Liu, Y.P. / Gao, A. / An, X.M. / Liu, S. / Yan, X.X. / Liang, D.C.
History
DepositionJan 6, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 19, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 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_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_seq_id / _struct_conn.ptnr1_label_seq_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

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Assembly

Deposited unit
A: Recombination protein recR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6292
Polymers23,5631
Non-polymers651
Water54030
1
A: Recombination protein recR
hetero molecules

A: Recombination protein recR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2574
Polymers47,1262
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_554-x+1/2,y,-z-1/21
Buried area4190 Å2
ΔGint-27 kcal/mol
Surface area22970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.848, 123.729, 135.203
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222

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Components

#1: Protein Recombination protein recR / Genetic recombination / RecR Recombinational DNA repair protein


Mass: 23563.145 Da / Num. of mol.: 1 / Mutation: K21G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacter tengcongensis (bacteria)
Strain: MB4 / Gene: recR / Production host: Escherichia coli (E. coli) / References: UniProt: Q8RDI4
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.97 Å3/Da / Density % sol: 58.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 8%(w/v) PEG4000, 200mM Ammonium Sulfate, 10%(v/v) 2-Propanol, 100mM HEPES Sodium Salt, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9875 Å
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9875 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 6949 / Biso Wilson estimate: 68.93 Å2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VDP

3vdp


Resolution: 2.8→19.724 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7004 / SU ML: 0.3 / σ(F): 0 / Phase error: 34.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2598 313 4.77 %RANDOM
Rwork0.223 6244 --
obs0.2248 6557 92.67 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80 Å2 / ksol: 0.313 e/Å3
Displacement parametersBiso max: 186.92 Å2 / Biso mean: 86.2895 Å2 / Biso min: 46.72 Å2
Baniso -1Baniso -2Baniso -3
1-53.8245 Å2-0 Å2-0 Å2
2---26.1432 Å20 Å2
3----18.3896 Å2
Refinement stepCycle: LAST / Resolution: 2.8→19.724 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1488 0 1 30 1519
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121510
X-RAY DIFFRACTIONf_angle_d1.5432044
X-RAY DIFFRACTIONf_chiral_restr0.092243
X-RAY DIFFRACTIONf_plane_restr0.005262
X-RAY DIFFRACTIONf_dihedral_angle_d18.376559
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-3.52440.35411360.30052979311589
3.5244-19.72470.23461770.20023265344296

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