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- PDB-4o6p: Structural and functional studies the characterization of C58G/C7... -

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Basic information

Entry
Database: PDB / ID: 4o6p
TitleStructural and functional studies the characterization of C58G/C70G mutant in Cys4 Zinc-finger motif in the recombination mediator protein RecR
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, 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 ...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 / Toprim domain profile. / TOPRIM domain / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Recombination protein RecR
Similarity search - Component
Biological speciesThermoanaerobacter tengcongensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsTang, Q. / Liu, Y.P. / Yan, X.X. / Liang, D.C.
CitationJournal: DNA Repair (Amst.) / Year: 2014
Title: Structural and functional characterization of Cys4 zinc finger motif in the recombination mediator protein RecR.
Authors: Tang, Q. / Liu, Y.P. / Yan, X.X. / Liang, D.C.
History
DepositionDec 23, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Database references / Category: citation / struct_ref_seq_dif
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _struct_ref_seq_dif.details
Revision 1.2Nov 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_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
B: Recombination protein RecR
C: Recombination protein RecR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2174
Polymers47,0862
Non-polymers1312
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-103 kcal/mol
Surface area23710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.862, 65.754, 91.755
Angle α, β, γ (deg.)90.00, 95.41, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-324-

HOH

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Components

#1: Protein Recombination protein RecR / RECR RECOMBINATIONAL DNA REPAIR PROTEIN


Mass: 23543.092 Da / Num. of mol.: 2 / Mutation: C58G/C70G
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.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.99 Å3/Da / Density % sol: 58.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.15
Details: 12%(W/V) PEG33500, 100MM SODIUM ACETATE, 2%(W/V) TACSIMATE, pH 5.15, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.005 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.005 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 10641

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Processing

Software
NameVersionClassification
PHASESphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VDP

3vdp


Resolution: 3→19.84 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.912 / SU B: 19.968 / SU ML: 0.365 / Cross valid method: THROUGHOUT / ESU R Free: 0.418
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.253 568 5.1 %RANDOM
Rwork0.235 ---
obs0.236 10641 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 72.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å20.08 Å2
2--0.08 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 3→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3047 0 2 71 3120
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223088
X-RAY DIFFRACTIONr_angle_refined_deg1.8581.9934175
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4545391
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.31924.228123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.10815576
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2611520
X-RAY DIFFRACTIONr_chiral_restr0.1210.2492
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212253
X-RAY DIFFRACTIONr_mcbond_it0.6821.51953
X-RAY DIFFRACTIONr_mcangle_it1.29523175
X-RAY DIFFRACTIONr_scbond_it1.67731135
X-RAY DIFFRACTIONr_scangle_it2.9124.51000
LS refinement shellResolution: 3→3.08 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 39 -
Rwork0.316 749 -
obs--99.75 %

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