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- PDB-4p4o: Crystal structure of Leishmania infantum polymerase beta: Ternary... -

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Basic information

Entry
Database: PDB / ID: 4p4o
TitleCrystal structure of Leishmania infantum polymerase beta: Ternary gap complex
Components
  • DNA (5'-D(*CP*AP*GP*TP*AP*T)-3')
  • DNA (5'-D(P*CP*GP*GP*CP*AP*AP*TP*AP*CP*TP*G)-3')
  • DNA (5'-D(P*GP*CP*CP*G)-3')
  • DNA polymerase beta
KeywordsTRANSFERASE/DNA / DNA polymerase / TRANSFERASE-DNA complex
Function / homology
Function and homology information


double-strand break repair via nonhomologous end joining / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding / nucleus / metal ion binding
Similarity search - Function
Beta Polymerase; domain 3 / DNA polymerase, thumb domain / DNA polymerase family X, beta-like / DNA polymerase beta, palm domain / DNA polymerase beta palm / DNA polymerase lambda, fingers domain / Fingers domain of DNA polymerase lambda / DNA-directed DNA polymerase X / DNA polymerase beta-like, N-terminal domain / Helix-hairpin-helix domain ...Beta Polymerase; domain 3 / DNA polymerase, thumb domain / DNA polymerase family X, beta-like / DNA polymerase beta, palm domain / DNA polymerase beta palm / DNA polymerase lambda, fingers domain / Fingers domain of DNA polymerase lambda / DNA-directed DNA polymerase X / DNA polymerase beta-like, N-terminal domain / Helix-hairpin-helix domain / DNA polymerase X family / DNA polymerase lambda lyase domain superfamily / DNA polymerase family X / DNA polymerase beta, thumb domain / DNA polymerase beta thumb / DNA polymerase, thumb domain superfamily / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase
Similarity search - Component
Biological speciesLeishmania infantum (eukaryote)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3001 Å
AuthorsMejia, E. / Burak, M. / Alonso, A. / Larraga, V. / Kunkel, T. / Bebenek, K. / Garcia-Diaz, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM100021-02 United States
CitationJournal: DNA Repair (Amst.) / Year: 2014
Title: Structures of the Leishmania infantum polymerase beta.
Authors: Mejia, E. / Burak, M. / Alonso, A. / Larraga, V. / Kunkel, T.A. / Bebenek, K. / Garcia-Diaz, M.
History
DepositionMar 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.ptnr1_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase beta
E: DNA (5'-D(*CP*AP*GP*TP*AP*T)-3')
G: DNA (5'-D(P*GP*CP*CP*G)-3')
F: DNA (5'-D(P*CP*GP*GP*CP*AP*AP*TP*AP*CP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8578
Polymers49,3214
Non-polymers5364
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint-51 kcal/mol
Surface area17510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.680, 108.680, 151.641
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-537-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA polymerase beta


Mass: 42962.488 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania infantum (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9U6N3

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DNA chain , 3 types, 3 molecules EGF

#2: DNA chain DNA (5'-D(*CP*AP*GP*TP*AP*T)-3')


Mass: 1808.229 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*GP*CP*CP*G)-3')


Mass: 1191.818 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(P*CP*GP*GP*CP*AP*AP*TP*AP*CP*TP*G)-3')


Mass: 3358.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 241 molecules

#5: Chemical ChemComp-D3T / 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE


Type: DNA OH 3 prime terminus / Mass: 466.169 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N2O13P3
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 2.65 Å3/Da / Density % sol: 53.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1 M magnesium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.3→94.13 Å / Num. obs: 24191 / % possible obs: 100 % / Redundancy: 21.3 % / Net I/σ(I): 31.4

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Processing

SoftwareName: PHENIX / Version: (PHENIX.REFINE: 1.7.1_743) / Classification: refinement
RefinementResolution: 2.3001→47.06 Å / SU ML: 0.62 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.228 1822 7.55 %
Rwork0.194 --
obs0.197 24157 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.76 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-8.823 Å20 Å20 Å2
2--8.823 Å20 Å2
3---6.9445 Å2
Refinement stepCycle: LAST / Resolution: 2.3001→47.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2387 387 31 237 3042
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082892
X-RAY DIFFRACTIONf_angle_d1.1253985
X-RAY DIFFRACTIONf_dihedral_angle_d17.551136
X-RAY DIFFRACTIONf_chiral_restr0.063439
X-RAY DIFFRACTIONf_plane_restr0.005449
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.38230.26091760.19792162X-RAY DIFFRACTION99
2.3823-2.47770.2471790.1962191X-RAY DIFFRACTION100
2.4777-2.59040.25721780.17962183X-RAY DIFFRACTION100
2.5904-2.7270.23591800.18482186X-RAY DIFFRACTION100
2.727-2.89780.23171780.17792197X-RAY DIFFRACTION100
2.8978-3.12150.24651810.18762205X-RAY DIFFRACTION100
3.1215-3.43550.23321820.17622230X-RAY DIFFRACTION100
3.4355-3.93250.19751840.17682243X-RAY DIFFRACTION100
3.9325-4.95360.19981860.17522289X-RAY DIFFRACTION100
4.9536-47.06960.24631980.25122426X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 1.2942 Å / Origin y: 35.1511 Å / Origin z: 70.7826 Å
111213212223313233
T0.1401 Å2-0.0016 Å2-0.0364 Å2-0.1921 Å2-0.0569 Å2--0.1219 Å2
L1.6841 °2-0.8817 °20.4758 °2-1.9807 °2-0.5261 °2--0.8179 °2
S-0.0254 Å °-0.3533 Å °0.0354 Å °0.2359 Å °0.0838 Å °0.025 Å °0.0117 Å °-0.1047 Å °-0.0644 Å °
Refinement TLS groupSelection details: ALL

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