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Basic information

Entry
Database: PDB / ID: 5iim
TitleCrystal structure of the pre-catalytic ternary extension complex of DNA polymerase lambda with an 8-oxo-dG:dA base-pair
Components
  • DNA (5'-D(*CP*AP*GP*TP*AP*A)-3')
  • DNA (5'-D(*CP*GP*GP*CP*AP*(8OG)P*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 beta-like, N-terminal domain ...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 beta-like, N-terminal domain / Helix-hairpin-helix domain / DNA polymerase X family / 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'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase lambda
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.941 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 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2016Group: Database references
Revision 1.2Sep 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 / citation / database_2 / pdbx_initial_refinement_model / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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*A)-3')
T: DNA (5'-D(*CP*GP*GP*CP*AP*(8OG)P*TP*AP*CP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2617
Polymers43,7484
Non-polymers5133
Water6,287349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6100 Å2
ΔGint-41 kcal/mol
Surface area17170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.274, 63.700, 140.725
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*A)-3')


Mass: 1817.244 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(*CP*GP*GP*CP*AP*(8OG)P*TP*AP*CP*TP*G)-3')


Mass: 3390.210 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 352 molecules

#5: Chemical ChemComp-DUP / 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O13P3
#6: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 349 / 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: 2.94 Å3/Da / Density % sol: 58.11 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium acetate, 0.1 M sodium citrate pH 4.8, and 3-5% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 17, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.94→58.03 Å / Num. obs: 36628 / % possible obs: 99.7 % / Redundancy: 5.8 % / CC1/2: 0.994 / Rmerge(I) obs: 0.076 / Net I/σ(I): 15.1
Reflection shellResolution: 1.941→1.947 Å / % possible obs: 99.7 % / Rmerge(I) obs: 0.766 / Mean I/σ(I) obs: 2.4 / CC1/2: 0.913

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XSN

1xsn


Resolution: 1.941→43.947 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2159 3597 9.97 %
Rwork0.1834 --
obs0.1866 36076 94.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.941→43.947 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2482 429 30 349 3290
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063055
X-RAY DIFFRACTIONf_angle_d0.8984234
X-RAY DIFFRACTIONf_dihedral_angle_d15.8821740
X-RAY DIFFRACTIONf_chiral_restr0.05469
X-RAY DIFFRACTIONf_plane_restr0.006472
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9407-1.96630.36061320.36481258X-RAY DIFFRACTION98
1.9663-1.99320.24561470.221301X-RAY DIFFRACTION100
1.9932-2.02170.24981590.1941309X-RAY DIFFRACTION100
2.0217-2.05180.20871550.17951288X-RAY DIFFRACTION100
2.0518-2.08390.22381440.1771308X-RAY DIFFRACTION100
2.0839-2.11810.21871460.17631289X-RAY DIFFRACTION100
2.1181-2.15460.25451370.17611313X-RAY DIFFRACTION100
2.1546-2.19380.24181490.19191291X-RAY DIFFRACTION100
2.1938-2.2360.321820.2543672X-RAY DIFFRACTION52
2.236-2.28160.4478770.4529722X-RAY DIFFRACTION57
2.2816-2.33120.2488870.1936777X-RAY DIFFRACTION100
2.3312-2.38540.20771440.17731298X-RAY DIFFRACTION100
2.3854-2.44510.21831540.16851332X-RAY DIFFRACTION100
2.4451-2.51120.19071400.16361290X-RAY DIFFRACTION100
2.5112-2.58510.19971620.16191296X-RAY DIFFRACTION100
2.5851-2.66850.21931430.16291336X-RAY DIFFRACTION100
2.6685-2.76390.20341410.1711323X-RAY DIFFRACTION100
2.7639-2.87450.22151460.17681311X-RAY DIFFRACTION100
2.8745-3.00530.18531440.1761328X-RAY DIFFRACTION100
3.0053-3.16370.18971500.17691347X-RAY DIFFRACTION100
3.1637-3.36190.22741480.1821316X-RAY DIFFRACTION100
3.3619-3.62130.20971340.16981344X-RAY DIFFRACTION100
3.6213-3.98550.26241490.2181342X-RAY DIFFRACTION99
3.9855-4.56170.15541500.13811351X-RAY DIFFRACTION100
4.5617-5.74530.15441420.14971385X-RAY DIFFRACTION100
5.7453-43.95870.21251350.18641352X-RAY DIFFRACTION92
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)
11.462-0.14330.63330.77670.05710.87970.02210.1798-0.0876-0.06930.0468-0.06920.03690.11340.01120.1196-0.01510.02450.1397-0.01340.1135-13.699511.3666-15.4868
20.030.00870.00190.0184-0.01980.02520.11550.02160.0432-0.09230.01020.1599-0.07030.10940.04620.28940.0046-0.01070.38660.11690.192-19.511829.108-29.7394
30.00830.0076-0.01470.0273-0.0210.0193-0.05680.01880.05640.1125-0.00650.07540.1691-0.0369-00.1418-0.00830.01470.1811-0.02580.1365-25.057315.1793-8.6927
40.1979-0.1135-0.09650.06060.05060.108-0.05470.1007-0.03010.00820.00280.2511-0.05430.0099-0.05610.2085-0.0009-0.01060.17990.00310.1628-27.015215.5777-17.4066
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 250 through 575)
2X-RAY DIFFRACTION2(chain 'D' and resid 1 through 4)
3X-RAY DIFFRACTION3(chain 'P' and resid 1 through 6)
4X-RAY DIFFRACTION4(chain 'T' and resid 1 through 11)

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