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- PDB-5lb3: Crystal structure of human RECQL5 helicase in complex with ADP/Mg. -

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Basic information

Entry
Database: PDB / ID: 5lb3
TitleCrystal structure of human RECQL5 helicase in complex with ADP/Mg.
ComponentsATP-dependent DNA helicase Q5
KeywordsHYDROLASE / Helicase / RecQ / Transcription / DNA repair / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


mitotic DNA-templated DNA replication / chromosome separation / cellular response to camptothecin / four-way junction helicase activity / replication-born double-strand break repair via sister chromatid exchange / DNA 3'-5' helicase / transcription preinitiation complex / DNA metabolic process / 3'-5' DNA helicase activity / DNA unwinding involved in DNA replication ...mitotic DNA-templated DNA replication / chromosome separation / cellular response to camptothecin / four-way junction helicase activity / replication-born double-strand break repair via sister chromatid exchange / DNA 3'-5' helicase / transcription preinitiation complex / DNA metabolic process / 3'-5' DNA helicase activity / DNA unwinding involved in DNA replication / negative regulation of transcription elongation by RNA polymerase II / RNA polymerase II complex binding / negative regulation of double-strand break repair via homologous recombination / DNA helicase activity / isomerase activity / replication fork / helicase activity / double-strand break repair via homologous recombination / cellular response to xenobiotic stimulus / mitotic cell cycle / chromosome / DNA replication / cell division / DNA repair / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
RecQ helicase-like 5 / RecQ helicase protein-like 5 (RecQ5) / ATP-dependent DNA helicase RecQ, zinc-binding domain / RecQ zinc-binding / DNA helicase, ATP-dependent, RecQ type / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain ...RecQ helicase-like 5 / RecQ helicase protein-like 5 (RecQ5) / ATP-dependent DNA helicase RecQ, zinc-binding domain / RecQ zinc-binding / DNA helicase, ATP-dependent, RecQ type / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / DEAD/DEAH box helicase / DEAD/DEAH box helicase 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 / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ATP-dependent DNA helicase Q5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsNewman, J.A. / Aitkenhead, H. / Savitsky, P. / Krojer, T. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Gileadi, O. / Structural Genomics Consortium (SGC)
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Insights into the RecQ helicase mechanism revealed by the structure of the helicase domain of human RECQL5.
Authors: Newman, J.A. / Aitkenhead, H. / Savitsky, P. / Gileadi, O.
History
DepositionJun 15, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2017Group: Database references
Revision 1.2Feb 1, 2017Group: Database references
Revision 1.3May 3, 2017Group: Database references
Revision 1.4Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.5Jan 10, 2024Group: 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
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_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: ATP-dependent DNA helicase Q5
E: ATP-dependent DNA helicase Q5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,1088
Polymers99,0742
Non-polymers1,0346
Water17,853991
1
B: ATP-dependent DNA helicase Q5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0544
Polymers49,5371
Non-polymers5173
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
E: ATP-dependent DNA helicase Q5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0544
Polymers49,5371
Non-polymers5173
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.757, 62.943, 104.703
Angle α, β, γ (deg.)90.00, 95.44, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ATP-dependent DNA helicase Q5 / DNA helicase / RecQ-like type 5 / RecQ5 / RecQ protein-like 5


Mass: 49537.180 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RECQL5, RECQ5 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O94762, DNA helicase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: 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
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 991 / 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: 2.41 Å3/Da / Density % sol: 48.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 23% PEG6K, 0.15M lithium chloride, 2.5% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.8→19.88 Å / Num. obs: 87336 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 20.7 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.078 / Net I/σ(I): 8.8
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.812 / Mean I/σ(I) obs: 1.3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1682refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CDG

4cdg


Resolution: 1.8→19.88 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / Phase error: 26.48
RfactorNum. reflection% reflectionSelection details
Rfree0.2335 4298 4.92 %Random
Rwork0.1949 ---
obs0.1968 87297 99.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6806 0 58 991 7855
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047074
X-RAY DIFFRACTIONf_angle_d0.7969593
X-RAY DIFFRACTIONf_dihedral_angle_d13.8912626
X-RAY DIFFRACTIONf_chiral_restr0.0281078
X-RAY DIFFRACTIONf_plane_restr0.0041233
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82040.34061270.30752798X-RAY DIFFRACTION100
1.8204-1.84180.34011460.31762719X-RAY DIFFRACTION100
1.8418-1.86430.30451390.30152759X-RAY DIFFRACTION100
1.8643-1.88790.36741380.28732733X-RAY DIFFRACTION100
1.8879-1.91270.36271480.29152764X-RAY DIFFRACTION100
1.9127-1.93890.3491680.27732706X-RAY DIFFRACTION100
1.9389-1.96650.31951400.26512782X-RAY DIFFRACTION100
1.9665-1.99590.28151350.24722700X-RAY DIFFRACTION100
1.9959-2.0270.29561560.24362768X-RAY DIFFRACTION100
2.027-2.06020.24431410.23122745X-RAY DIFFRACTION100
2.0602-2.09570.27451320.22092779X-RAY DIFFRACTION100
2.0957-2.13380.23741530.21572741X-RAY DIFFRACTION100
2.1338-2.17480.25541540.21132745X-RAY DIFFRACTION100
2.1748-2.21910.25291460.21372735X-RAY DIFFRACTION100
2.2191-2.26730.24611110.2132800X-RAY DIFFRACTION100
2.2673-2.320.281430.20672737X-RAY DIFFRACTION100
2.32-2.37790.25391190.20682793X-RAY DIFFRACTION100
2.3779-2.44210.26311260.20712800X-RAY DIFFRACTION100
2.4421-2.51380.25781380.22773X-RAY DIFFRACTION100
2.5138-2.59480.23081670.20062767X-RAY DIFFRACTION100
2.5948-2.68730.24661380.1992746X-RAY DIFFRACTION100
2.6873-2.79460.24981510.19662744X-RAY DIFFRACTION100
2.7946-2.92140.24521390.19352797X-RAY DIFFRACTION100
2.9214-3.07490.2291600.19672745X-RAY DIFFRACTION100
3.0749-3.26680.22891620.19352765X-RAY DIFFRACTION100
3.2668-3.51770.19131340.17942793X-RAY DIFFRACTION100
3.5177-3.86940.21581550.16822776X-RAY DIFFRACTION100
3.8694-4.42390.17711290.14862806X-RAY DIFFRACTION100
4.4239-5.55350.18721550.16152817X-RAY DIFFRACTION100
5.5535-19.880.19371480.16142866X-RAY DIFFRACTION99

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