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- PDB-4q47: Structure of the DrRecQ Catalytic Core in complex with ADP -

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Basic information

Entry
Database: PDB / ID: 4q47
TitleStructure of the DrRecQ Catalytic Core in complex with ADP
ComponentsDNA helicase RecQ
KeywordsDNA BINDING PROTEIN / DNA unwinding / Topoisomerase / helicase
Function / homology
Function and homology information


bacterial nucleoid / SOS response / replisome / DNA 3'-5' helicase / 3'-5' DNA helicase activity / isomerase activity / chromosome / single-stranded 3'-5' DNA helicase activity / double-stranded DNA helicase activity / forked DNA-dependent helicase activity ...bacterial nucleoid / SOS response / replisome / DNA 3'-5' helicase / 3'-5' DNA helicase activity / isomerase activity / chromosome / single-stranded 3'-5' DNA helicase activity / double-stranded DNA helicase activity / forked DNA-dependent helicase activity / four-way junction helicase activity / DNA recombination / DNA replication / hydrolase activity / DNA repair / DNA binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
DNA helicase, ATP-dependent, RecQ type, bacterial / RQC domain / RQC / RQC domain / Helicase and RNase D C-terminal / HRDC domain / HRDC domain / HRDC domain profile. / ATP-dependent DNA helicase RecQ, zinc-binding domain / RecQ zinc-binding ...DNA helicase, ATP-dependent, RecQ type, bacterial / RQC domain / RQC / RQC domain / Helicase and RNase D C-terminal / HRDC domain / HRDC domain / HRDC domain profile. / ATP-dependent DNA helicase RecQ, zinc-binding domain / RecQ zinc-binding / DNA helicase, ATP-dependent, RecQ type / HRDC domain superfamily / HRDC-like superfamily / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Arc Repressor Mutant, subunit A / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleotide triphosphate hydrolases / Winged helix-like DNA-binding domain superfamily / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / DNA helicase RecQ
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.899 Å
AuthorsChen, S.C. / Yang, C.S. / Chen, Y.
CitationJournal: Biomed Res Int / Year: 2014
Title: Crystal structure of Deinococcus radiodurans RecQ helicase catalytic core domain: the interdomain flexibility.
Authors: Chen, S.C. / Huang, C.H. / Yang, C.S. / Way, T.D. / Chang, M.C. / Chen, Y.
History
DepositionApr 14, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_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: DNA helicase RecQ
B: DNA helicase RecQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,8046
Polymers116,8192
Non-polymers9854
Water00
1
A: DNA helicase RecQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9023
Polymers58,4101
Non-polymers4932
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DNA helicase RecQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9023
Polymers58,4101
Non-polymers4932
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.756, 95.610, 183.832
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 DNA helicase RecQ


Mass: 58409.527 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1-517
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
Gene: DR_1289 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RUU2
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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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: 3.19 Å3/Da / Density % sol: 61.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 0.1M midazole (pH7.2), 16% PEG 20K, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.9762 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 30, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.899→30 Å / Num. all: 33844 / Num. obs: 33811 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.9→3 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.678 / Num. unique all: 3294 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OYW

1oyw


Resolution: 2.899→27.56 Å / SU ML: 0.49 / σ(F): 1.35 / Phase error: 33.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2953 1999 5.92 %10
Rwork0.2223 ---
all0.2265 33811 --
obs0.2265 33750 99.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.899→27.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7943 0 56 0 7999
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0128187
X-RAY DIFFRACTIONf_angle_d1.78711077
X-RAY DIFFRACTIONf_dihedral_angle_d16.7633056
X-RAY DIFFRACTIONf_chiral_restr0.2621247
X-RAY DIFFRACTIONf_plane_restr0.0081445
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8993-2.97170.40151370.3282217597
2.9717-3.05190.46461390.29792227100
3.0519-3.14160.39181420.27472250100
3.1416-3.24290.39861410.26362235100
3.2429-3.35860.3261410.24542249100
3.3586-3.49280.31781420.26232244100
3.4928-3.65140.35121420.25532252100
3.6514-3.84350.38591430.23962268100
3.8435-4.08350.27671410.2312254100
4.0835-4.39770.2791440.22281100
4.3977-4.83810.26711430.20062275100
4.8381-5.53320.27241450.21282292100
5.5332-6.95270.28131470.23812339100
6.9527-27.56130.23311520.1778241099

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