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- PDB-3e1s: Structure of an N-terminal truncation of Deinococcus radiodurans RecD2 -

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Basic information

Entry
Database: PDB / ID: 3e1s
TitleStructure of an N-terminal truncation of Deinococcus radiodurans RecD2
ComponentsExodeoxyribonuclease V, subunit RecD
KeywordsHYDROLASE / alpha and beta protein / ATP-binding / Nucleotide-binding
Function / homology
Function and homology information


exodeoxyribonuclease V complex / DNA 5'-3' helicase / single-stranded DNA helicase activity / ATP-dependent activity, acting on DNA / 5'-3' DNA helicase activity / DNA recombination / ATP hydrolysis activity / DNA binding / ATP binding
Similarity search - Function
Arc Repressor Mutant, subunit A - #2220 / SH3 type barrels. - #940 / RecD-like DNA helicase / RecD helicase-like helix-hairpin-helix domain / RecD-like DNA helicase, SH3 domain / : / ATP-dependent RecD2 DNA helicase HHH domain / ATP-dependent RecD-like DNA helicase SH3 domain / ATP-dependent DNA helicase YrrC, OB-fold domain / UvrD-like helicase C-terminal domain ...Arc Repressor Mutant, subunit A - #2220 / SH3 type barrels. - #940 / RecD-like DNA helicase / RecD helicase-like helix-hairpin-helix domain / RecD-like DNA helicase, SH3 domain / : / ATP-dependent RecD2 DNA helicase HHH domain / ATP-dependent RecD-like DNA helicase SH3 domain / ATP-dependent DNA helicase YrrC, OB-fold domain / UvrD-like helicase C-terminal domain / UvrD-like helicase C-terminal domain / AAA domain / Helix-hairpin-helix domain / SH3 type barrels. / : / Arc Repressor Mutant, subunit A / Roll / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ATP-dependent RecD2 DNA helicase
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.2 Å
AuthorsSaikrishnan, K. / Griffiths, S.P. / Cook, N. / Court, R. / Wigley, D.B.
CitationJournal: Embo J. / Year: 2008
Title: DNA binding to RecD: role of the 1B domain in SF1B helicase activity.
Authors: Saikrishnan, K. / Griffiths, S.P. / Cook, N. / Court, R. / Wigley, D.B.
History
DepositionAug 4, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Exodeoxyribonuclease V, subunit RecD


Theoretical massNumber of molelcules
Total (without water)61,4661
Polymers61,4661
Non-polymers00
Water4,774265
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.630, 89.630, 131.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Exodeoxyribonuclease V, subunit RecD


Mass: 61465.914 Da / Num. of mol.: 1
Fragment: N-terminus deletion mutant of RecD2, UNP residues 151-715
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Gene: recD / Plasmid: pET22B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9RT63
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.62 Å3/Da / Density % sol: 53.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 13-18% ethanol, 100mM Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.07225 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 3, 2007
RadiationMonochromator: Single Silicon (111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07225 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 33616 / Num. obs: 32947 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.038 / Net I/σ(I): 15.2
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 2.25 % / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 3.2 / Num. unique all: 4035 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DNAdata collection
XDSdata reduction
XDSdata scaling
SHARPphasing
RefinementMethod to determine structure: MIR / Resolution: 2.2→20.7 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.911 / SU B: 16.458 / SU ML: 0.219 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.29 / ESU R Free: 0.242 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28744 2668 8.1 %RANDOM
Rwork0.2308 ---
all0.23541 32946 --
obs0.23541 30278 98.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.288 Å2
Baniso -1Baniso -2Baniso -3
1-3.38 Å20 Å20 Å2
2---4.09 Å20 Å2
3---0.71 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3889 0 0 265 4154
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0213962
X-RAY DIFFRACTIONr_bond_other_d0.0020.022671
X-RAY DIFFRACTIONr_angle_refined_deg1.2461.9725382
X-RAY DIFFRACTIONr_angle_other_deg0.88936493
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7595513
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.96322.934167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.94215636
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7191537
X-RAY DIFFRACTIONr_chiral_restr0.070.2619
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024463
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02789
X-RAY DIFFRACTIONr_nbd_refined0.2010.2971
X-RAY DIFFRACTIONr_nbd_other0.20.22870
X-RAY DIFFRACTIONr_nbtor_refined0.1690.21906
X-RAY DIFFRACTIONr_nbtor_other0.0880.22177
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.205
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.146
X-RAY DIFFRACTIONr_symmetry_vdw_other0.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.095
X-RAY DIFFRACTIONr_mcbond_it0.499
X-RAY DIFFRACTIONr_mcbond_other0.092
X-RAY DIFFRACTIONr_mcangle_it0.607
X-RAY DIFFRACTIONr_scbond_it1.004
X-RAY DIFFRACTIONr_scangle_it1.515
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 181 -
Rwork0.284 2161 -
obs--97.54 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.22641.0467-1.64145.48653.785713.32980.0301-0.40770.75220.2057-0.25860.353-1.8931-1.3040.22850.30330.1817-0.1215-0.1632-0.025-0.0828-2.4868-7.529547.6344
21.94082.0984.28556.63044.800612.38980.189-0.1575-0.3672-0.0020.1279-0.37291.12690.1461-0.3169-0.0913-0.0071-0.0558-0.2290.0578-0.1636-0.6743-27.244934.5342
31.19560.48660.81865.0759-0.86984.35480.05370.0378-0.0794-0.79440.25220.33230.9875-0.5318-0.3059-0.0187-0.164-0.1371-0.19330.0557-0.1889-11.0239-23.860315.6866
43.7022-0.2033-0.15376.84740.27273.7087-0.11940.08780.1685-0.7578-0.1354-0.2767-0.03190.1920.2547-0.2771-0.0673-0.0015-0.23040.0564-0.2425-2.45422.53811.9518
57.45151.29761.201314.7457-1.5065.57370.2555-0.59940.21440.3567-0.22651.1295-0.169-0.7545-0.0291-0.35640.01370.02690.2383-0.0980.1674-25.77523.012122.3798
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA193 - 27444 - 125
2X-RAY DIFFRACTION2AA275 - 322126 - 173
3X-RAY DIFFRACTION2AA704 - 720555 - 571
4X-RAY DIFFRACTION3AA339 - 491190 - 342
5X-RAY DIFFRACTION4AA492 - 574343 - 425
6X-RAY DIFFRACTION4AA640 - 703491 - 554
7X-RAY DIFFRACTION5AA575 - 639426 - 490

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