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- PDB-2v1x: Crystal structure of human RECQ-like DNA helicase -

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Basic information

Entry
Database: PDB / ID: 2v1x
TitleCrystal structure of human RECQ-like DNA helicase
ComponentsATP-DEPENDENT DNA HELICASE Q1
KeywordsHYDROLASE / DNA STRAND ANNEALING / MISMATCH REPAIR / NUCLEOTIDE-BINDING / DNA-BINDING / NUCLEAR PROTEIN / ATPASE / HELICASE / ATP-BINDING
Function / homology
Function and homology information


double-stranded DNA helicase activity / DNA/DNA annealing activity / four-way junction helicase activity / mediator complex / DNA 3'-5' helicase / replication fork processing / DNA unwinding involved in DNA replication / 3'-5' DNA helicase activity / DNA helicase activity / isomerase activity ...double-stranded DNA helicase activity / DNA/DNA annealing activity / four-way junction helicase activity / mediator complex / DNA 3'-5' helicase / replication fork processing / DNA unwinding involved in DNA replication / 3'-5' DNA helicase activity / DNA helicase activity / isomerase activity / double-strand break repair via homologous recombination / chromosome / DNA repair / ATP hydrolysis activity / nucleoplasm / ATP binding / membrane / nucleus / metal ion binding / cytoplasm
Similarity search - Function
RQC domain / ATP-dependent DNA helicase RecQ, zinc-binding domain / RecQ zinc-binding / DNA helicase, ATP-dependent, RecQ type / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / 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. ...RQC domain / ATP-dependent DNA helicase RecQ, zinc-binding domain / RecQ zinc-binding / DNA helicase, ATP-dependent, RecQ type / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / 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 / Helicase superfamily 1/2, ATP-binding domain / Arc Repressor Mutant, subunit A / P-loop containing nucleotide triphosphate hydrolases / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ATP-dependent DNA helicase Q1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPike, A.C.W. / Shrestha, B. / Burgess-Brown, N. / King, O. / Ugochukwu, E. / Watt, S. / Edwards, A. / Arrowsmith, C.H. / Weigelt, J. / Sundstrom, M. / Gileadi, O.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Structure of the Human Recq1 Helicase Reveals a Putative Strand-Separation Pin.
Authors: Pike, A.C.W. / Shrestha, B. / Popuri, V. / Burgess-Brown, N. / Muzzolini, L. / Costantini, S. / Vindigni, A. / Gileadi, O.
History
DepositionMay 30, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2007Provider: repository / Type: Initial release
Revision 1.1Jan 21, 2015Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Structure summary / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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_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_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_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_conn.ptnr2_label_seq_id / _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: ATP-DEPENDENT DNA HELICASE Q1
B: ATP-DEPENDENT DNA HELICASE Q1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,24719
Polymers134,7702
Non-polymers1,47717
Water5,675315
1
A: ATP-DEPENDENT DNA HELICASE Q1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0448
Polymers67,3851
Non-polymers6597
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ATP-DEPENDENT DNA HELICASE Q1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,20311
Polymers67,3851
Non-polymers81810
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)83.229, 97.647, 85.849
Angle α, β, γ (deg.)90.00, 104.50, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A65 - 161
2115B18 - 161
1215A184 - 224
2215B184 - 224
1315A230 - 281
2315B230 - 281

NCS oper: (Code: given
Matrix: (1, 0.017, -0.001), (-0.017, 1, -0.004), (0.001, 0.004, 1)
Vector: -22.28387, 49.27942, 8.24779)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein ATP-DEPENDENT DNA HELICASE Q1 / DNA-DEPENDENT ATPASE Q1 / RECQ DNA HELICASE


Mass: 67384.938 Da / Num. of mol.: 2 / Fragment: RESIDUES 49-616
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC-CTHF / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2
References: UniProt: P46063, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides

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Non-polymers , 6 types, 332 molecules

#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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / 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: 2.51 Å3/Da / Density % sol: 51.01 %
Crystal growpH: 7.5
Details: 0.2M SODIUM BROMIDE,20% PEG3350, 10% ETHYLENE GLYCOL, 0.1M BIS TRIS PROPANE PH7.5, pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.03315
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 16, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03315 Å / Relative weight: 1
ReflectionResolution: 2→45.74 Å / Num. obs: 89784 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 31.96 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.4
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 1.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.3.0037refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OYY

1oyy


Resolution: 2→45 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.931 / SU B: 6.493 / SU ML: 0.174 / Cross valid method: THROUGHOUT / ESU R: 0.195 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.278 4497 5 %RANDOM
Rwork0.232 ---
obs0.235 85242 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.88 Å2
Baniso -1Baniso -2Baniso -3
1--2.33 Å20 Å2-0.1 Å2
2--4.6 Å20 Å2
3----2.31 Å2
Refinement stepCycle: LAST / Resolution: 2→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8148 0 75 315 8538
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0228490
X-RAY DIFFRACTIONr_bond_other_d0.0010.025654
X-RAY DIFFRACTIONr_angle_refined_deg1.4391.9611519
X-RAY DIFFRACTIONr_angle_other_deg0.923.00113826
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.60751072
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.24124.202357
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.47151456
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6671542
X-RAY DIFFRACTIONr_chiral_restr0.0830.21307
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029399
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021715
X-RAY DIFFRACTIONr_nbd_refined0.1990.21736
X-RAY DIFFRACTIONr_nbd_other0.190.25837
X-RAY DIFFRACTIONr_nbtor_refined0.180.24085
X-RAY DIFFRACTIONr_nbtor_other0.0890.24417
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2040.2430
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1720.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1980.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.80535499
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.13758532
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.34583515
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.626112978
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1128medium positional0.130.5
2B1128medium positional0.130.5
1A1311loose positional0.325
2B1311loose positional0.325
1A1128medium thermal0.722
2B1128medium thermal0.722
1A1311loose thermal0.8110
2B1311loose thermal0.8110
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.416 338
Rwork0.349 6217

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