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- PDB-3vdp: Structure and biochemical studies of the recombination mediator p... -

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Basic information

Entry
Database: PDB / ID: 3vdp
TitleStructure and biochemical studies of the recombination mediator protein RecR in RecFOR pathway
ComponentsRecombination protein recR
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 / DNA recombination protein RecR / Recombination protein RecR, conserved site / Recombination protein RecR / RecR, TOPRIM domain / RecR, Cys4-zinc finger motif / RecR, helix-hairpin-helix ...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 / DNA recombination protein RecR / Recombination protein RecR, conserved site / Recombination protein RecR / RecR, TOPRIM domain / RecR, Cys4-zinc finger motif / RecR, helix-hairpin-helix / 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
IMIDAZOLE / Recombination protein RecR
Similarity search - Component
Biological speciesThermoanaerobacter tengcongensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.451 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 5, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 19, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 20, 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_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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_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

Downloads & links

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Assembly

Deposited unit
A: Recombination protein recR
B: Recombination protein recR
C: Recombination protein recR
D: Recombination protein recR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,21714
Polymers94,5414
Non-polymers67610
Water5,855325
1
A: Recombination protein recR
B: Recombination protein recR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6788
Polymers47,2712
Non-polymers4076
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-30 kcal/mol
Surface area22730 Å2
MethodPISA
2
C: Recombination protein recR
D: Recombination protein recR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5406
Polymers47,2712
Non-polymers2694
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-30 kcal/mol
Surface area23120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.260, 68.325, 94.056
Angle α, β, γ (deg.)90.00, 92.95, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 23635.273 Da / Num. of mol.: 4
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.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / 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: 3.06 Å3/Da / Density % sol: 59.85 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.9875 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9875 Å / Relative weight: 1
ReflectionResolution: 2.45→20 Å / Num. obs: 41210 / Biso Wilson estimate: 39.56 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 / Resolution: 2.451→19.963 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7763 / SU ML: 0.33 / σ(F): 1.35 / Phase error: 28.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2265 2072 5.03 %RANDOM
Rwork0.196 ---
obs0.1976 41210 97.56 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.306 Å2 / ksol: 0.312 e/Å3
Displacement parametersBiso max: 149.65 Å2 / Biso mean: 54.649 Å2 / Biso min: 14.79 Å2
Baniso -1Baniso -2Baniso -3
1--12.5133 Å20 Å23.4273 Å2
2--21.4745 Å20 Å2
3----9.0225 Å2
Refinement stepCycle: LAST / Resolution: 2.451→19.963 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6122 0 34 325 6481
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0136249
X-RAY DIFFRACTIONf_angle_d1.5668434
X-RAY DIFFRACTIONf_chiral_restr0.111996
X-RAY DIFFRACTIONf_plane_restr0.0071075
X-RAY DIFFRACTIONf_dihedral_angle_d19.4462386
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4506-2.5380.30991870.2633425361286
2.538-2.63940.33952020.27223915411798
2.6394-2.75920.33991960.26083936413298
2.7592-2.90430.2662140.23453924413899
2.9043-3.08560.26662250.2423903412899
3.0856-3.32290.25052370.2253955419299
3.3229-3.65540.24791910.21433975416699
3.6554-4.18020.18622080.16743987419599
4.1802-5.25070.16142050.13864032423799
5.2507-19.9640.19922070.1744086429399

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