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- PDB-5a9j: Crystal structure of the Helicase domain of human DNA polymerase ... -

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Basic information

Entry
Database: PDB / ID: 5a9j
TitleCrystal structure of the Helicase domain of human DNA polymerase theta, apo-form
ComponentsDNA POLYMERASE THETAPOLQ
KeywordsHYDROLASE / POLYMERASE / HELICASE / POLQ / DNA REPAIR
Function / homology
Function and homology information


single-stranded DNA endodeoxyribonuclease activity / double-strand break repair via alternative nonhomologous end joining / HDR through MMEJ (alt-NHEJ) / single-stranded DNA helicase activity / negative regulation of double-strand break repair via homologous recombination / replication fork processing / site of DNA damage / 5'-deoxyribose-5-phosphate lyase activity / somatic hypermutation of immunoglobulin genes / error-prone translesion synthesis ...single-stranded DNA endodeoxyribonuclease activity / double-strand break repair via alternative nonhomologous end joining / HDR through MMEJ (alt-NHEJ) / single-stranded DNA helicase activity / negative regulation of double-strand break repair via homologous recombination / replication fork processing / site of DNA damage / 5'-deoxyribose-5-phosphate lyase activity / somatic hypermutation of immunoglobulin genes / error-prone translesion synthesis / DNA helicase activity / base-excision repair / protein homooligomerization / RNA-directed DNA polymerase / RNA-directed DNA polymerase activity / double-strand break repair / site of double-strand break / DNA helicase / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA repair / DNA damage response / chromatin binding / Golgi apparatus / magnesium ion binding / ATP hydrolysis activity / nucleoplasm / ATP binding / identical protein binding / cytosol
Similarity search - Function
DNA polymerase theta-like, helix-turn-helix domain / : / Helix-turn-helix domain / DNA_pol_Q helicase like region helical domain / DNA polymerase A / DNA polymerase family A / DNA-directed DNA polymerase, family A, conserved site / DNA polymerase family A signature. / DNA-directed DNA polymerase, family A, palm domain / DNA polymerase A domain ...DNA polymerase theta-like, helix-turn-helix domain / : / Helix-turn-helix domain / DNA_pol_Q helicase like region helical domain / DNA polymerase A / DNA polymerase family A / DNA-directed DNA polymerase, family A, conserved site / DNA polymerase family A signature. / DNA-directed DNA polymerase, family A, palm domain / DNA polymerase A domain / 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 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA polymerase theta
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.55 Å
AuthorsNewman, J.A. / Cooper, C.D.O. / Aitkenhead, H. / Pinkas, D.M. / Kupinska, K. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Gileadi, O.
CitationJournal: Structure / Year: 2015
Title: Structure of the Helicase Domain of DNA Polymerase Theta Reveals a Possible Role in the Microhomology-Mediated End-Joining Pathway.
Authors: Newman, J.A. / Cooper, C.D.O. / Aitkenhead, H. / Gileadi, O.
History
DepositionJul 21, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA POLYMERASE THETA
B: DNA POLYMERASE THETA
C: DNA POLYMERASE THETA
D: DNA POLYMERASE THETA


Theoretical massNumber of molelcules
Total (without water)400,0834
Polymers400,0834
Non-polymers00
Water0
1
A: DNA POLYMERASE THETA


Theoretical massNumber of molelcules
Total (without water)100,0211
Polymers100,0211
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DNA POLYMERASE THETA


Theoretical massNumber of molelcules
Total (without water)100,0211
Polymers100,0211
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: DNA POLYMERASE THETA


Theoretical massNumber of molelcules
Total (without water)100,0211
Polymers100,0211
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: DNA POLYMERASE THETA


Theoretical massNumber of molelcules
Total (without water)100,0211
Polymers100,0211
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)128.017, 130.531, 160.910
Angle α, β, γ (deg.)90.00, 100.77, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
DNA POLYMERASE THETA / POLQ / DNA POLYMERASE ETA


Mass: 100020.812 Da / Num. of mol.: 4 / Fragment: HELICASE DOMAIN, UNP RESIDUES 1-894
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: O75417
Sequence detailsFIRST TWO RESIDUES REMAIN AFTER CLEAVAGE OF PURIFICATION TAG

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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: 3.5 Å3/Da / Density % sol: 65 % / Description: NONE
Crystal growDetails: 0.2M NACL, 20% PEG 6K, 10% ETHYLENE GLYCOL, 0.1 M HEPES PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 3.55→48.8 Å / Num. obs: 62574 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 129.69 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.8
Reflection shellResolution: 3.55→3.64 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 1.8 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5AGA

5aga


Resolution: 3.55→48.861 Å / SU ML: 0.55 / σ(F): 0.03 / Phase error: 30.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.265 5989 4.9 %
Rwork0.2249 --
obs0.2269 62469 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 150 Å2
Refinement stepCycle: LAST / Resolution: 3.55→48.861 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24408 0 0 0 24408
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00424843
X-RAY DIFFRACTIONf_angle_d0.98133646
X-RAY DIFFRACTIONf_dihedral_angle_d13.8379056
X-RAY DIFFRACTIONf_chiral_restr0.0393968
X-RAY DIFFRACTIONf_plane_restr0.0054239
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5501-3.59040.40682130.3473866X-RAY DIFFRACTION100
3.5904-3.63260.48921830.37193877X-RAY DIFFRACTION99
3.6326-3.67690.49662080.43233653X-RAY DIFFRACTION94
3.6769-3.72340.43491680.38843867X-RAY DIFFRACTION97
3.7234-3.77240.35141950.31753880X-RAY DIFFRACTION99
3.7724-3.82410.36342020.31783887X-RAY DIFFRACTION99
3.8241-3.87870.34352070.32193901X-RAY DIFFRACTION100
3.8787-3.93650.32122130.30013863X-RAY DIFFRACTION99
3.9365-3.9980.31241820.28213983X-RAY DIFFRACTION100
3.998-4.06350.31312280.28053850X-RAY DIFFRACTION100
4.0635-4.13360.31121640.27173972X-RAY DIFFRACTION100
4.1336-4.20870.29051930.27053879X-RAY DIFFRACTION100
4.2087-4.28960.27522490.26293865X-RAY DIFFRACTION100
4.2896-4.37710.25071730.24983912X-RAY DIFFRACTION100
4.3771-4.47220.30432090.24593949X-RAY DIFFRACTION100
4.4722-4.57620.28921610.23483936X-RAY DIFFRACTION100
4.5762-4.69050.27072020.22773905X-RAY DIFFRACTION100
4.6905-4.81730.23841820.2263933X-RAY DIFFRACTION100
4.8173-4.95890.26421960.22243880X-RAY DIFFRACTION100
4.9589-5.11880.2871980.22033915X-RAY DIFFRACTION100
5.1188-5.30150.27842060.22443918X-RAY DIFFRACTION100
5.3015-5.51350.2852030.23653905X-RAY DIFFRACTION100
5.5135-5.76410.29462300.24483872X-RAY DIFFRACTION100
5.7641-6.06740.32282120.2333877X-RAY DIFFRACTION99
6.0674-6.44680.23512060.21983897X-RAY DIFFRACTION99
6.4468-6.94320.27572080.22023884X-RAY DIFFRACTION100
6.9432-7.63960.24862050.20163925X-RAY DIFFRACTION99
7.6396-8.73960.21011840.15713879X-RAY DIFFRACTION99
8.7396-10.99030.15182270.13213828X-RAY DIFFRACTION99
10.9903-48.86560.23261820.18883852X-RAY DIFFRACTION98

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