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- PDB-5lba: Crystal structure of human RECQL5 helicase in complex with DSPL f... -

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Basic information

Entry
Database: PDB / ID: 5lba
TitleCrystal structure of human RECQL5 helicase in complex with DSPL fragment(1-cyclohexyl-3-(oxolan-2-ylmethyl)urea, SGC - Diamond XChem I04-1 fragment screening.
ComponentsATP-dependent DNA helicase Q5
KeywordsHYDROLASE / Helicase / RecQ / Transcription / Fragment screening / Structural Genomics / Structural Genomics Consortium / SGC / DIAMOND I04-1 XCHEM"
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 / replication fork / isomerase activity / 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) / Set2 Rpb1 interacting domain / SRI (Set2 Rpb1 interacting) domain / 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 domain ...RecQ helicase-like 5 / RecQ helicase protein-like 5 (RecQ5) / Set2 Rpb1 interacting domain / SRI (Set2 Rpb1 interacting) domain / 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 domain / DEAD/DEAH box helicase / 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
1-cyclohexyl-3-[[(2~{R})-oxolan-2-yl]methyl]urea / ADENOSINE-5'-DIPHOSPHATE / ATP-dependent DNA helicase Q5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.5 Å
AuthorsNewman, J.A. / Aitkenhead, H. / Talon, R. / 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: To be published
Title: Crystal structure of human RECQL5 helicase in complex with 3D fragment (1-cyclohexyl-3-(oxolan-2-ylmethyl)urea)
Authors: Newman, J.A. / Talon, R. / Aitkenhead, H. / Savitsky, P. / Krojer, T. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Gileadi, O.
History
DepositionJun 15, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.2Jan 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
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
A: ATP-dependent DNA helicase Q5
C: ATP-dependent DNA helicase Q5
D: ATP-dependent DNA helicase Q5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,67720
Polymers198,1494
Non-polymers2,52816
Water6,089338
1
B: ATP-dependent DNA helicase Q5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3596
Polymers49,5371
Non-polymers8215
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: ATP-dependent DNA helicase Q5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1325
Polymers49,5371
Non-polymers5954
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 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
4
D: ATP-dependent DNA helicase Q5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1325
Polymers49,5371
Non-polymers5954
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.926, 85.261, 105.915
Angle α, β, γ (deg.)109.90, 90.02, 97.01
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules BACD

#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.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RECQL5, RECQ5 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: O94762, DNA helicase

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Non-polymers , 6 types, 354 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-6SV / 1-cyclohexyl-3-[[(2~{R})-oxolan-2-yl]methyl]urea


Mass: 226.315 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H22N2O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.72 Å3/Da / Density % sol: 54.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M tris pH 9.0 -- 29% PEG3350 -- 0.1M sodium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 2.47→79.49 Å / Num. obs: 69069 / % possible obs: 92.3 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 5.8
Reflection shellResolution: 2.47→2.53 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.513 / Mean I/σ(I) obs: 1.3 / % possible all: 94.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5LB5

5lb5


Resolution: 2.5→79.49 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.863 / SU B: 15.593 / SU ML: 0.329 / Cross valid method: THROUGHOUT / ESU R: 0.829 / ESU R Free: 0.37 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30292 3363 5 %RANDOM
Rwork0.23665 ---
obs0.24 63558 92.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 48.293 Å2
Baniso -1Baniso -2Baniso -3
1--0.92 Å2-1.61 Å2-0.7 Å2
2--1.47 Å21.54 Å2
3----1.02 Å2
Refinement stepCycle: 1 / Resolution: 2.5→79.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13429 0 144 338 13911
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01913879
X-RAY DIFFRACTIONr_bond_other_d0.0020.0213357
X-RAY DIFFRACTIONr_angle_refined_deg1.4961.97418798
X-RAY DIFFRACTIONr_angle_other_deg0.958330661
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.67551732
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.66823.057592
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.231152366
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.26215115
X-RAY DIFFRACTIONr_chiral_restr0.0740.22122
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02115588
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023215
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.0624.7276946
X-RAY DIFFRACTIONr_mcbond_other3.0624.7276945
X-RAY DIFFRACTIONr_mcangle_it4.9427.0778672
X-RAY DIFFRACTIONr_mcangle_other4.9417.0778673
X-RAY DIFFRACTIONr_scbond_it2.9064.9986933
X-RAY DIFFRACTIONr_scbond_other2.9064.9986934
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8317.37110127
X-RAY DIFFRACTIONr_long_range_B_refined7.6836.61515044
X-RAY DIFFRACTIONr_long_range_B_other7.6836.61815045
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.496→2.561 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 264 -
Rwork0.33 4818 -
obs--93.95 %

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