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- PDB-4p4m: Crystal structure of Leishmania infantum polymerase beta: Ternary... -

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Basic information

Entry
Database: PDB / ID: 4p4m
TitleCrystal structure of Leishmania infantum polymerase beta: Ternary P/T complex
Components
  • DNA (5'-D(*CP*AP*GP*TP*A)-3')
  • DNA (5'-D(P*AP*TP*AP*CP*TP*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 polymerase
Similarity search - Component
Biological speciesLeishmania infantum (eukaryote)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9185 Å
AuthorsMejia, E. / Burak, M. / Alonso, A. / Larraga, V. / Kunkel, T.A. / 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 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 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 / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
D: DNA (5'-D(*CP*AP*GP*TP*A)-3')
E: DNA (5'-D(P*AP*TP*AP*CP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7886
Polymers46,2753
Non-polymers5133
Water5,873326
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-32 kcal/mol
Surface area14560 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-531-

HOH

21A-555-

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 , 2 types, 2 molecules DE

#2: DNA chain DNA (5'-D(*CP*AP*GP*TP*A)-3')


Mass: 1504.037 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*AP*TP*AP*CP*TP*G)-3')


Mass: 1808.229 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 329 molecules

#4: 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
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 326 / 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: 2.79 Å3/Da / Density % sol: 55.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 120 mM magnesium chloride, 0.4 M Tris-HCl, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.075 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: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.918→94.13 Å / Num. obs: 41119 / % possible obs: 100 % / Redundancy: 18.7 % / Net I/σ(I): 38.4
Reflection shellResolution: 1.918→1.948 Å / % possible obs: 100 % / Mean I/σ(I) obs: 4.1 / Rsym value: 0.613 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
CBASSdata collection
HKL-2000data scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BPY

1bpy


Resolution: 1.9185→44.945 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 16.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1815 3100 7.55 %
Rwork0.1639 --
obs0.1653 41054 99.95 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9185→44.945 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2102 224 30 326 2682
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142502
X-RAY DIFFRACTIONf_angle_d1.2923443
X-RAY DIFFRACTIONf_dihedral_angle_d15.647984
X-RAY DIFFRACTIONf_chiral_restr0.071377
X-RAY DIFFRACTIONf_plane_restr0.004410
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9185-1.94850.23291360.18661663X-RAY DIFFRACTION99
1.9485-1.98040.19631370.17381689X-RAY DIFFRACTION100
1.9804-2.01460.17671390.16811698X-RAY DIFFRACTION100
2.0146-2.05120.16971390.17031704X-RAY DIFFRACTION100
2.0512-2.09070.18031380.16141689X-RAY DIFFRACTION100
2.0907-2.13330.18271380.1571687X-RAY DIFFRACTION100
2.1333-2.17970.17891390.16361697X-RAY DIFFRACTION100
2.1797-2.23040.1881380.16851692X-RAY DIFFRACTION100
2.2304-2.28620.25331390.16971700X-RAY DIFFRACTION100
2.2862-2.3480.18521400.17161714X-RAY DIFFRACTION100
2.348-2.41710.21451400.17241718X-RAY DIFFRACTION100
2.4171-2.49510.1951390.16631695X-RAY DIFFRACTION100
2.4951-2.58430.19521400.16561719X-RAY DIFFRACTION100
2.5843-2.68770.18621410.17391715X-RAY DIFFRACTION100
2.6877-2.810.1921400.16811719X-RAY DIFFRACTION100
2.81-2.95820.17021410.16781728X-RAY DIFFRACTION100
2.9582-3.14350.20811420.16611725X-RAY DIFFRACTION100
3.1435-3.38610.17461430.15751755X-RAY DIFFRACTION100
3.3861-3.72670.14471420.1451751X-RAY DIFFRACTION100
3.7267-4.26560.1261450.13231768X-RAY DIFFRACTION100
4.2656-5.37280.16611470.15291801X-RAY DIFFRACTION100
5.3728-44.95760.22471570.20271927X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.37841.17690.51376.37541.71713.31110.0328-1.13520.42230.70950.2619-0.1683-0.26120.5529-0.28470.3564-0.03770.01690.7602-0.18750.3717-3.9517-19.682511.4984
22.0873-0.7152-0.59810.88910.26581.31520.0541-0.0730.01150.0529-0.04040.092-0.1111-0.0659-0.01780.18670.0050.04150.119-0.00710.1554-8.497-34.1001-9.3048
32.5706-0.0381-1.29564.148-1.2633.0684-0.0007-0.1543-0.06060.2341-0.0281-0.28470.0550.27550.01010.16690.0318-0.02370.1589-0.0040.150311.0457-46.3236-9.5346
45.8851-3.6715-4.1886.1217-1.37247.12470.2817-1.03690.13440.0312-0.18970.0503-0.18890.2821-0.08950.241-0.0736-0.03980.41940.02070.26383.01-26.68030.4207
52.8841-1.10870.16054.3128-0.51592.42920.0794-0.23180.39670.3135-0.0138-0.2167-0.27510.1655-0.0750.2197-0.04360.04020.2032-0.02220.21956.7601-31.481-5.0266
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 90 through 117 )
2X-RAY DIFFRACTION2chain 'A' and (resid 118 through 304 )
3X-RAY DIFFRACTION3chain 'A' and (resid 305 through 376 )
4X-RAY DIFFRACTION4chain 'D' and (resid 1 through 5 )
5X-RAY DIFFRACTION5chain 'E' and (resid 6 through 11 )

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