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- PDB-3gp8: Crystal structure of the binary complex of RecD2 with DNA -

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Basic information

Entry
Database: PDB / ID: 3gp8
TitleCrystal structure of the binary complex of RecD2 with DNA
Components
  • 5'-D(*TP*TP*TP*TP*TP*T*TP*TP*TP*TP*TP*TP*TP*T)-3'
  • Exodeoxyribonuclease V, subunit RecD, putative
KeywordsHYDROLASE/DNA / ALPHA AND BETA PROTEIN / ATP-BINDING / NUCLEOTIDE-BINDING / HELICASE / HYDROLASE-DNA COMPLEX
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
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 ...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. / : / 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 / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / ATP-dependent RecD2 DNA helicase
Similarity search - Component
Biological speciesDeinococcus radiodurans R1 (radioresistant)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSaikrishnan, K. / Cook, N. / Wigley, D.B.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 2009
Title: Mechanistic basis of 5'-3' translocation in SF1B helicases.
Authors: Saikrishnan, K. / Powell, B. / Cook, N.J. / Webb, M.R. / Wigley, D.B.
#1: Journal: 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
DepositionMar 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Sep 6, 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 / struct_ref_seq / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Exodeoxyribonuclease V, subunit RecD, putative
X: 5'-D(*TP*TP*TP*TP*TP*T*TP*TP*TP*TP*TP*TP*TP*T)-3'


Theoretical massNumber of molelcules
Total (without water)65,6802
Polymers65,6802
Non-polymers00
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-24.4 kcal/mol
Surface area25700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.140, 90.320, 142.180
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, putative


Mass: 61465.914 Da / Num. of mol.: 1 / Fragment: UNP residues 151-715
Source method: isolated from a genetically manipulated source
Details: N-terminus deletion mutant of RecD2
Source: (gene. exp.) Deinococcus radiodurans R1 (radioresistant)
Strain: R1 / DSM 20539 / IFO 15346 / LMG 4051 / NCIB 9279 / Gene: DR_1902, recD / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9RT63
#2: DNA chain 5'-D(*TP*TP*TP*TP*TP*T*TP*TP*TP*TP*TP*TP*TP*T)-3'


Mass: 4213.742 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic DNA
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 2.65 Å3/Da / Density % sol: 53.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 15% PEG 8000, 2-6% Ethylene glycol, 100mM Tris-HCl pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 800011
2Ethylene glycol11
3Tris-HCl11
4PEG 800012
5Ethylene glycol12
6Tris-HCl12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 20, 2008 / Details: mirrors
RadiationMonochromator: Varimax / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 24877 / Num. obs: 24589 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Rmerge(I) obs: 0.032 / Rsym value: 0.032 / Net I/σ(I): 33.7
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.175 / Mean I/σ(I) obs: 8 / Num. unique all: 2492 / Rsym value: 0.175 / % possible all: 91.8

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.2.0019refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3E1S

3e1s


Resolution: 2.5→45.18 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.905 / SU ML: 0.237 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.519 / ESU R Free: 0.299 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26827 1256 5.1 %RANDOM
Rwork0.22815 ---
all0.23023 23332 --
obs0.23023 23332 98.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.8 Å2
Refinement stepCycle: LAST / Resolution: 2.5→45.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4088 157 0 190 4435
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0214329
X-RAY DIFFRACTIONr_bond_other_d0.0020.022870
X-RAY DIFFRACTIONr_angle_refined_deg1.1462.025910
X-RAY DIFFRACTIONr_angle_other_deg0.88536976
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2125546
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.77922.604169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.7515659
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9461542
X-RAY DIFFRACTIONr_chiral_restr
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024779
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02850
X-RAY DIFFRACTIONr_nbd_refined0.220.21028
X-RAY DIFFRACTIONr_nbd_other0.1960.23073
X-RAY DIFFRACTIONr_nbtor_refined0.1760.22047
X-RAY DIFFRACTIONr_nbtor_other0.0860.22358
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2162
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0450.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1950.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2080.23
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_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.57 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 92 -
Rwork0.296 1555 -
obs--89.75 %
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)
11.3149-0.0202-0.09982.30010.53042.2183-0.07490.2824-0.0533-0.2490.01290.2034-0.0749-0.22160.062-0.28490.0611-0.0769-0.20550.0169-0.1578-13.98379.5636-42.4718
22.4151-0.38430.38794.53380.49294.5404-0.1142-0.17560.01240.9552-0.0290.121-0.3863-0.17770.1432-0.043-0.00950.0198-0.2480-0.2409-0.956922.6366-16.1142
33.9332.1845-1.21526.9531-0.36523.24180.2525-0.3854-0.21861.5393-0.2607-0.61690.19770.24740.00830.11450.0183-0.1239-0.20050.0413-0.18929.1763-5.0031-15.1831
46.3091-8.4254-0.033119.4287-7.4296.8301-0.6407-0.7304-0.88492.35580.78982.41090.1982-1.3588-0.14910.7684-0.09170.64120.29970.05060.416-14.4194-8.4169-8.9057
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A154 - 322
2X-RAY DIFFRACTION2A327 - 489
3X-RAY DIFFRACTION2A701 - 716
4X-RAY DIFFRACTION3A490 - 575
5X-RAY DIFFRACTION3A636 - 700
6X-RAY DIFFRACTION4A576 - 635

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