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- PDB-4o6o: Structural and functional studies the characterization of Cys4 Zi... -

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Basic information

Entry
Database: PDB / ID: 4o6o
TitleStructural and functional studies the characterization of 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
IMIDAZOLE / 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 / 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_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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_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
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)94,82611
Polymers94,3574
Non-polymers4697
Water2,378132
1
A: Recombination protein RecR
B: Recombination protein RecR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5167
Polymers47,1782
Non-polymers3385
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4810 Å2
ΔGint-103 kcal/mol
Surface area22750 Å2
MethodPISA
2
C: Recombination protein RecR
D: Recombination protein RecR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3094
Polymers47,1782
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-71 kcal/mol
Surface area22620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.604, 67.912, 94.364
Angle α, β, γ (deg.)90.00, 92.98, 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: 23589.184 Da / Num. of mol.: 4 / Mutation: C55Y
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.: 3 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 3.07 Å3/Da / Density % sol: 59.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 8%(W/V) PEG3350, 200MM LITHIUM CITRIC TRIBASIC TETRAHYDRATE, 100MM MES, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

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: 2.7→20 Å / Num. obs: 21645

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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→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.945 / SU B: 37.334 / SU ML: 0.349 / Cross valid method: THROUGHOUT / ESU R Free: 0.42 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1156 5.1 %RANDOM
Rwork0.22 ---
obs0.222 21645 98.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 76.9 Å2
Baniso -1Baniso -2Baniso -3
1--3.24 Å20 Å22.45 Å2
2--6.72 Å20 Å2
3----3.23 Å2
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6058 0 19 132 6209
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0226168
X-RAY DIFFRACTIONr_angle_refined_deg1.9461.9938338
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2755786
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.66624.009232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.118151139
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0881539
X-RAY DIFFRACTIONr_chiral_restr0.1150.2993
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214470
X-RAY DIFFRACTIONr_mcbond_it3.9451.53929
X-RAY DIFFRACTIONr_mcangle_it7.15126383
X-RAY DIFFRACTIONr_scbond_it5.18532239
X-RAY DIFFRACTIONr_scangle_it9.354.51955
X-RAY DIFFRACTIONr_rigid_bond_restr3.30136146
LS refinement shellResolution: 3→3.08 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.417 84 -
Rwork0.353 1582 -
obs--98.87 %

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