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- PDB-5zvq: Crystal structure of recombination mediator protein RecR -

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Basic information

Entry
Database: PDB / ID: 5zvq
TitleCrystal structure of recombination mediator protein RecR
ComponentsRecombination protein RecR
KeywordsRECOMBINATION / recombination mediator protein
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 / 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 speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsChaudhary, S.K. / Sekar, K. / Jeyakanthan, J.
CitationJournal: To Be Published
Title: Crystal structure of recombination mediator protein RecR
Authors: Chaudhary, S.K. / Sekar, K. / Jeyakanthan, J.
History
DepositionMay 12, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)21,3373
Polymers21,2361
Non-polymers1012
Water54030
1
A: Recombination protein RecR
hetero molecules

A: Recombination protein RecR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6756
Polymers42,4732
Non-polymers2024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area4700 Å2
ΔGint-61 kcal/mol
Surface area22000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.920, 100.220, 136.020
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Recombination protein RecR


Mass: 21236.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / Gene: recR, TTHA1600
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q5SHY0
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / 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: 2.89 Å3/Da / Density % sol: 57.5 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 7.5
Details: 0.2 M Potassium chloride, 0.05 M HEPES pH 7.5, 35% v/v Pentaerythritol propoxylate (5/4 PO/OH)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.5417 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5417 Å / Relative weight: 1
ReflectionResolution: 2.5→80.68 Å / Num. obs: 8602 / % possible obs: 96.8 % / Redundancy: 10.3 % / Net I/σ(I): 14.6
Reflection shellResolution: 2.5→2.6 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
PDB_EXTRACT3.22data extraction
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VDD

1vdd


Resolution: 2.5→80.68 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.926 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.495 / ESU R Free: 0.31
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2828 426 5 %RANDOM
Rwork0.2361 ---
obs0.2384 8176 96.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 123.06 Å2 / Biso mean: 76.335 Å2 / Biso min: 43.16 Å2
Baniso -1Baniso -2Baniso -3
1--4.04 Å2-0 Å20 Å2
2---0.54 Å2-0 Å2
3---4.58 Å2
Refinement stepCycle: final / Resolution: 2.5→80.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1444 0 2 30 1476
Biso mean--83.78 65.26 -
Num. residues----194
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0191473
X-RAY DIFFRACTIONr_bond_other_d00.021435
X-RAY DIFFRACTIONr_angle_refined_deg1.1142.0121994
X-RAY DIFFRACTIONr_angle_other_deg3.76333292
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7545195
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.632260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.48715248
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.011518
X-RAY DIFFRACTIONr_chiral_restr0.0560.2231
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211664
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02302
X-RAY DIFFRACTIONr_mcbond_it2.6167.671777
X-RAY DIFFRACTIONr_mcbond_other2.6167.671776
X-RAY DIFFRACTIONr_mcangle_it4.27111.504970
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 18 -
Rwork0.332 587 -
all-605 -
obs--90.98 %

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