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- PDB-5iij: Crystal structure of the pre-catalytic ternary complex of DNA pol... -

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Basic information

Entry
Database: PDB / ID: 5iij
TitleCrystal structure of the pre-catalytic ternary complex of DNA polymerase lambda with a templating 8-oxo-dG and an incoming dCTP
Components
  • DNA (5'-D(*CP*AP*GP*TP*AP*(DOC))-3')
  • DNA (5'-D(*CP*GP*GP*CP*(8OG)P*GP*TP*AP*CP*TP*G)-3')
  • DNA (5'-D(P*GP*CP*CP*G)-3')
  • DNA polymerase lambda
KeywordsTRANSFERASE/DNA / TRANSFERASE-DNA COMPLEX
Function / homology
Function and homology information


DNA biosynthetic process / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / 5'-deoxyribose-5-phosphate lyase activity / somatic hypermutation of immunoglobulin genes / base-excision repair, gap-filling / nucleotide-excision repair / Nonhomologous End-Joining (NHEJ) / double-strand break repair via homologous recombination / double-strand break repair via nonhomologous end joining / site of double-strand break ...DNA biosynthetic process / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / 5'-deoxyribose-5-phosphate lyase activity / somatic hypermutation of immunoglobulin genes / base-excision repair, gap-filling / nucleotide-excision repair / Nonhomologous End-Joining (NHEJ) / double-strand break repair via homologous recombination / double-strand break repair via nonhomologous end joining / site of double-strand break / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA replication / DNA binding / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
Beta Polymerase; domain 3 / DNA polymerase, thumb domain / DNA polymerase family X, beta-like / DNA polymerase beta, N-terminal domain-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 X family ...Beta Polymerase; domain 3 / DNA polymerase, thumb domain / DNA polymerase family X, beta-like / DNA polymerase beta, N-terminal domain-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 X family / DNA polymerase beta-like, N-terminal domain / Helix-hairpin-helix domain / DNA polymerase family X, binding site / DNA polymerase family X signature. / 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 / BRCT domain profile. / BRCT domain / BRCT domain superfamily / 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'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase lambda
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.724 Å
AuthorsBurak, M.J. / Guja, K.E. / Garcia-Diaz, M.
CitationJournal: Embo J. / Year: 2016
Title: A fidelity mechanism in DNA polymerase lambda promotes error-free bypass of 8-oxo-dG.
Authors: Burak, M.J. / Guja, K.E. / Hambardjieva, E. / Derkunt, B. / Garcia-Diaz, M.
History
DepositionMar 1, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2016Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_conn_type
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _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 / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase lambda
D: DNA (5'-D(P*GP*CP*CP*G)-3')
P: DNA (5'-D(*CP*AP*GP*TP*AP*(DOC))-3')
T: DNA (5'-D(*CP*GP*GP*CP*(8OG)P*GP*TP*AP*CP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2458
Polymers43,7244
Non-polymers5214
Water7,368409
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6250 Å2
ΔGint-42 kcal/mol
Surface area16510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.749, 62.850, 140.076
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA polymerase lambda / Pol Lambda / DNA polymerase beta-2 / Pol beta2 / DNA polymerase kappa


Mass: 37348.559 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9UGP5, DNA-directed DNA polymerase, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases

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DNA chain , 3 types, 3 molecules DPT

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


Mass: 1777.219 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(*CP*GP*GP*CP*(8OG)P*GP*TP*AP*CP*TP*G)-3')


Mass: 3406.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 413 molecules

#5: Chemical ChemComp-DCT / 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE


Type: DNA linking / Mass: 451.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O12P3
#6: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 409 / 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: 2.87 Å3/Da / Density % sol: 57.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium cacodylate pH 7.0 and 1.0 M sodium acetate trihydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.724→70.038 Å / Num. all: 52778 / Num. obs: 52702 / % possible obs: 100 % / Redundancy: 7.2 % / Net I/σ(I): 22.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 1.724→41.706 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.35
RfactorNum. reflection% reflection
Rfree0.224 2598 4.93 %
Rwork0.1969 --
obs0.1982 52694 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.724→41.706 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2388 427 30 409 3254
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072942
X-RAY DIFFRACTIONf_angle_d1.0714074
X-RAY DIFFRACTIONf_dihedral_angle_d17.4831084
X-RAY DIFFRACTIONf_chiral_restr0.043450
X-RAY DIFFRACTIONf_plane_restr0.005450
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7244-1.75580.27681370.25972620X-RAY DIFFRACTION100
1.7558-1.78950.27831300.25032601X-RAY DIFFRACTION100
1.7895-1.82610.25671240.23962594X-RAY DIFFRACTION100
1.8261-1.86580.26471530.23452587X-RAY DIFFRACTION100
1.8658-1.90920.26221510.23972612X-RAY DIFFRACTION100
1.9092-1.95690.28711250.23982577X-RAY DIFFRACTION100
1.9569-2.00980.24291420.21262599X-RAY DIFFRACTION100
2.0098-2.0690.2531380.20892607X-RAY DIFFRACTION100
2.069-2.13570.2411080.20732641X-RAY DIFFRACTION100
2.1357-2.21210.23691330.20252624X-RAY DIFFRACTION100
2.2121-2.30060.23621400.20992599X-RAY DIFFRACTION100
2.3006-2.40530.2471560.2122623X-RAY DIFFRACTION100
2.4053-2.53210.26721390.21352616X-RAY DIFFRACTION100
2.5321-2.69070.24611190.2132666X-RAY DIFFRACTION100
2.6907-2.89840.22131510.21172635X-RAY DIFFRACTION100
2.8984-3.190.22551300.19932658X-RAY DIFFRACTION100
3.19-3.65140.21461360.18162699X-RAY DIFFRACTION100
3.6514-4.59940.18351380.16222703X-RAY DIFFRACTION100
4.5994-41.71830.19191480.17522835X-RAY DIFFRACTION99

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