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- PDB-5h45: Crystal structure of the C-terminal Lon protease-like domain of T... -

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Basic information

Entry
Database: PDB / ID: 5h45
TitleCrystal structure of the C-terminal Lon protease-like domain of Thermus thermophilus RadA/Sms
ComponentsDNA repair protein RadA
KeywordsDNA BINDING PROTEIN / Ribosomal protein S5 domain 2-like fold
Function / homology
Function and homology information


recombinational repair / ATP-dependent activity, acting on DNA / damaged DNA binding / hydrolase activity / ATP binding / metal ion binding
Similarity search - Function
DNA repair protein RadA / Subunit ChlI of Mg-chelatase / LapB, rubredoxin metal binding domain / Rubredoxin metal binding domain / DNA recombination and repair protein RecA-like, ATP-binding domain / RecA family profile 1. / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA repair protein RadA
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsInoue, M. / Fukui, K. / Fujii, Y. / Nakagawa, N. / Yano, T. / Kuramitsu, S. / Masui, R.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: The Lon protease-like domain in the bacterial RecA paralog RadA is required for DNA binding and repair.
Authors: Inoue, M. / Fukui, K. / Fujii, Y. / Nakagawa, N. / Yano, T. / Kuramitsu, S. / Masui, R.
History
DepositionOct 30, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: DNA repair protein RadA
B: DNA repair protein RadA


Theoretical massNumber of molelcules
Total (without water)39,2672
Polymers39,2672
Non-polymers00
Water93752
1
A: DNA repair protein RadA
B: DNA repair protein RadA

A: DNA repair protein RadA
B: DNA repair protein RadA

A: DNA repair protein RadA
B: DNA repair protein RadA


Theoretical massNumber of molelcules
Total (without water)117,8026
Polymers117,8026
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area10020 Å2
ΔGint-36 kcal/mol
Surface area36420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.289, 156.289, 156.289
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332

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Components

#1: Protein DNA repair protein RadA


Mass: 19633.619 Da / Num. of mol.: 2 / Fragment: UNP residues 262-423
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / Gene: radA, TTHA0541 / Plasmid: pET-HisTEV / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3) / References: UniProt: Q5SKV2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 4.05 Å3/Da / Density % sol: 69.64 %
Crystal growTemperature: 277.15 K / Method: batch mode / pH: 7.5
Details: 4mg/mL protein, 50mM Tris-HCl, 500mM sodium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Feb 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 18550 / % possible obs: 100 % / Redundancy: 41.3 % / Net I/σ(I): 20.4
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 41.6 % / Mean I/σ(I) obs: 1.9 / CC1/2: 0.625 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→49.42 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.911 / SU B: 8.581 / SU ML: 0.176 / Cross valid method: THROUGHOUT / ESU R: 0.289 / ESU R Free: 0.251 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24997 947 5.1 %RANDOM
Rwork0.19648 ---
obs0.19908 17548 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 53.493 Å2
Refinement stepCycle: 1 / Resolution: 2.7→49.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2288 0 0 52 2340
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192319
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6222.0173148
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8695307
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.48121.48994
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.02215375
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5061533
X-RAY DIFFRACTIONr_chiral_restr0.0940.2372
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211759
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 76 -
Rwork0.267 1109 -
obs--100 %

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