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- PDB-4p4p: Crystal structure of Leishmania infantum polymerase beta: Nick complex -

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Basic information

Entry
Database: PDB / ID: 4p4p
TitleCrystal structure of Leishmania infantum polymerase beta: Nick complex
Components
  • DNA (5'-D(*CP*AP*GP*TP*AP*CP*T)-3')
  • DNA (5'-D(P*CP*GP*GP*CP*AP*GP*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 / metal ion binding / nucleus
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, thumb domain superfamily / DNA polymerase beta thumb / 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
DNA / DNA (> 10) / DNA polymerase
Similarity search - Component
Biological speciesLeishmania infantum (eukaryote)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2973 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 ...Author supporting evidence / Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _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 1.3Sep 27, 2023Group: 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 / refine_hist / 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.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 / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)49,6495
Polymers49,6264
Non-polymers231
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-35 kcal/mol
Surface area16190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.497, 106.497, 159.609
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-527-

HOH

21A-542-

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 CDB

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


Mass: 2097.411 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*GP*TP*AP*CP*TP*G)-3')


Mass: 3374.210 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 251 molecules

#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 277 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium sulfate, 0.1 M sodium acetate, pH 4.6 and 12.5% PEG 4000

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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: 2.297→50 Å / Num. obs: 24544 / % possible obs: 100 % / Redundancy: 7.8 % / Net I/σ(I): 20.9

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BPY

1bpy


Resolution: 2.2973→44.303 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2338 1997 8.16 %
Rwork0.1912 --
obs0.1948 24483 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2973→44.303 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2219 386 1 250 2856
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062705
X-RAY DIFFRACTIONf_angle_d1.0453730
X-RAY DIFFRACTIONf_dihedral_angle_d18.5911058
X-RAY DIFFRACTIONf_chiral_restr0.064412
X-RAY DIFFRACTIONf_plane_restr0.005420
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2973-2.35480.27321370.21311536X-RAY DIFFRACTION98
2.3548-2.41840.23721410.21221591X-RAY DIFFRACTION100
2.4184-2.48960.26961390.1861567X-RAY DIFFRACTION100
2.4896-2.56990.20971400.17731574X-RAY DIFFRACTION100
2.5699-2.66180.20851410.18331583X-RAY DIFFRACTION100
2.6618-2.76830.21781390.18961561X-RAY DIFFRACTION100
2.7683-2.89430.2591410.19151586X-RAY DIFFRACTION100
2.8943-3.04690.2691420.20171605X-RAY DIFFRACTION100
3.0469-3.23770.24751420.21521593X-RAY DIFFRACTION100
3.2377-3.48760.23311430.18221607X-RAY DIFFRACTION100
3.4876-3.83840.23441440.18171612X-RAY DIFFRACTION100
3.8384-4.39340.19811440.16561626X-RAY DIFFRACTION100
4.3934-5.53350.20361480.17661661X-RAY DIFFRACTION100
5.5335-44.31070.26471560.22331784X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -2.978 Å / Origin y: -34.8218 Å / Origin z: -8.3482 Å
111213212223313233
T0.1832 Å20.0018 Å20.0389 Å2-0.1342 Å20.0084 Å2--0.1402 Å2
L1.2033 °2-0.5622 °2-0.6819 °2-0.9346 °20.3895 °2--0.6783 °2
S0.1093 Å °-0.0669 Å °0.0329 Å °0.063 Å °-0.0528 Å °0.0153 Å °-0.0646 Å °0.0016 Å °-0.0444 Å °
Refinement TLS groupSelection details: chain 'A' and (resid 32 through 376 )

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