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- PDB-3gpl: Crystal structure of the ternary complex of RecD2 with DNA and ADPNP -

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Basic information

Entry
Database: PDB / ID: 3gpl
TitleCrystal structure of the ternary complex of RecD2 with DNA and ADPNP
Components
  • 5'-D(*T*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
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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / DNA / 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: Version format compliance
Revision 1.2Sep 6, 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_ref_seq_dif / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_ref_seq_dif.details / _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: Exodeoxyribonuclease V, subunit RecD, putative
B: Exodeoxyribonuclease V, subunit RecD, putative
X: 5'-D(*T*TP*TP*TP*TP*TP*TP*T)-3'
Y: 5'-D(*T*TP*TP*TP*TP*TP*TP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,7708
Polymers127,7094
Non-polymers1,0614
Water3,351186
1
A: Exodeoxyribonuclease V, subunit RecD, putative
X: 5'-D(*T*TP*TP*TP*TP*TP*TP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3854
Polymers63,8542
Non-polymers5312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-19 kcal/mol
Surface area22790 Å2
MethodPISA
2
B: Exodeoxyribonuclease V, subunit RecD, putative
Y: 5'-D(*T*TP*TP*TP*TP*TP*TP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3854
Polymers63,8542
Non-polymers5312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-19.3 kcal/mol
Surface area22760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.120, 130.360, 80.050
Angle α, β, γ (deg.)90.00, 107.34, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Exodeoxyribonuclease V, subunit RecD, putative


Mass: 61465.914 Da / Num. of mol.: 2 / 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, recD2 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9RT63
#2: DNA chain 5'-D(*T*TP*TP*TP*TP*TP*TP*T)-3'


Mass: 2388.585 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic DNA
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.58 Å3/Da / Density % sol: 52.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 10% PEG 8000, 100 mM Tris-HCl pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 800011
2Tris-HCl11
3PEG 800012
4Tris-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: 44807 / Num. obs: 44090 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 2.3 % / Biso Wilson estimate: 27.2 Å2 / Rmerge(I) obs: 0.047 / Rsym value: 0.047 / Net I/σ(I): 16.05
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 2 % / Rmerge(I) obs: 0.251 / Mean I/σ(I) obs: 3.83 / Num. unique all: 4633 / Rsym value: 0.251 / % possible all: 94.6

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
CNS1.2refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3E1S

3e1s


Resolution: 2.5→43.27 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1445846.88 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.273 2234 5.1 %RANDOM
Rwork0.232 ---
obs0.232 44090 98.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.1733 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 45.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.75 Å20 Å23 Å2
2---8.04 Å20 Å2
3---8.79 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.48 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.5→43.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7798 274 64 186 8322
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.353 364 5.1 %
Rwork0.325 6814 -
obs--96.5 %

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