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- PDB-3c5g: Structure of a ternary complex of the R517K Pol lambda mutant -

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Basic information

Entry
Database: PDB / ID: 3c5g
TitleStructure of a ternary complex of the R517K Pol lambda mutant
Components
  • DNA (5'-D(*DCP*DAP*DGP*DTP*DAP*(2DT))-3')
  • DNA (5'-D(*DCP*DGP*DGP*DCP*DAP*DAP*DTP*DAP*DCP*DTP*DG)-3')
  • DNA (5'-D(P*DGP*DCP*DCP*DG)-3')
  • DNA polymerase lambda
KeywordsTransferase/DNA / Lyase/DNA / helix-hairpin-helix / DNA damage / DNA repair / DNA replication / DNA synthesis / DNA-binding / DNA-directed DNA polymerase / Lyase / Manganese / Metal-binding / Nucleotidyltransferase / Nucleus / Phosphoprotein / Transferase / Lyase-DNA COMPLEX / Transferase-DNA
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 replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding / nucleoplasm / nucleus / metal ion binding
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 lambda lyase domain superfamily / DNA polymerase family X, binding site / DNA polymerase family X signature. / 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 / 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'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase lambda
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsGarcia-Diaz, M. / Bebenek, K. / Foley, M.C. / Pedersen, L.C. / Schlick, T. / Kunkel, T.A.
CitationJournal: Embo Rep. / Year: 2008
Title: Substrate-induced DNA strand misalignment during catalytic cycling by DNA polymerase lambda.
Authors: Bebenek, K. / Garcia-Diaz, M. / Foley, M.C. / Pedersen, L.C. / Schlick, T. / Kunkel, T.A.
History
DepositionJan 31, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 11, 2017Group: Other
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase lambda
T: DNA (5'-D(*DCP*DGP*DGP*DCP*DAP*DAP*DTP*DAP*DCP*DTP*DG)-3')
P: DNA (5'-D(*DCP*DAP*DGP*DTP*DAP*(2DT))-3')
D: DNA (5'-D(P*DGP*DCP*DCP*DG)-3')
B: DNA polymerase lambda
U: DNA (5'-D(*DCP*DGP*DGP*DCP*DAP*DAP*DTP*DAP*DCP*DTP*DG)-3')
Q: DNA (5'-D(*DCP*DAP*DGP*DTP*DAP*(2DT))-3')
E: DNA (5'-D(P*DGP*DCP*DCP*DG)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,81521
Polymers87,5888
Non-polymers1,22713
Water15,097838
1
A: DNA polymerase lambda
T: DNA (5'-D(*DCP*DGP*DGP*DCP*DAP*DAP*DTP*DAP*DCP*DTP*DG)-3')
P: DNA (5'-D(*DCP*DAP*DGP*DTP*DAP*(2DT))-3')
D: DNA (5'-D(P*DGP*DCP*DCP*DG)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,43811
Polymers43,7944
Non-polymers6457
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA polymerase lambda
U: DNA (5'-D(*DCP*DGP*DGP*DCP*DAP*DAP*DTP*DAP*DCP*DTP*DG)-3')
Q: DNA (5'-D(*DCP*DAP*DGP*DTP*DAP*(2DT))-3')
E: DNA (5'-D(P*DGP*DCP*DCP*DG)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,37610
Polymers43,7944
Non-polymers5826
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.335, 150.819, 85.822
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 37451.734 Da / Num. of mol.: 2 / Fragment: DNA binding region / Mutation: R517K
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-CodonPlus-RIL
References: UniProt: Q9UGP5, DNA-directed DNA polymerase, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases

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DNA chain , 3 types, 6 molecules TUPQDE

#2: DNA chain DNA (5'-D(*DCP*DGP*DGP*DCP*DAP*DAP*DTP*DAP*DCP*DTP*DG)-3')


Mass: 3358.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Template
#3: DNA chain DNA (5'-D(*DCP*DAP*DGP*DTP*DAP*(2DT))-3')


Mass: 1792.230 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Primer
#4: DNA chain DNA (5'-D(P*DGP*DCP*DCP*DG)-3')


Mass: 1191.818 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Downstream Primer

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Non-polymers , 5 types, 851 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-D3T / 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE


Type: DNA OH 3 prime terminus / Mass: 466.169 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N2O13P3
#8: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 838 / 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: 3.49 Å3/Da / Density % sol: 64.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M KCl, 10 mM MgCl2, 50 mM Tris-HCl, pH 8.5 and 30% PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1KCl11
2MgCl211
3Tris-HCl11
4PEG 4011
5KCl12
6MgCl212
7Tris-HCl12
8PEG 4012

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: Nov 23, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 60372 / % possible obs: 96.8 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.091 / Χ2: 1.067 / Net I/σ(I): 11.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.2-2.282.60.4155061.108189.6
2.28-2.374.20.3856511.115192
2.37-2.484.60.33157641.121193.5
2.48-2.614.80.25959291.108195.9
2.61-2.775.20.20660381.072197.5
2.77-2.995.60.15961241.097199.2
2.99-3.296.10.10762311.062199.9
3.29-3.766.80.07362711.0261100
3.76-4.747.60.06463021.0131100
4.74-508.80.05965561.062199.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.004data extraction
HKL-2000data collection
HKL-2000data reduction
CNSphasing
RefinementResolution: 2.2→50 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.236 2806 4.5 %
Rwork0.201 --
obs-55423 88.2 %
Solvent computationBsol: 40.873 Å2
Displacement parametersBiso mean: 28.125 Å2
Baniso -1Baniso -2Baniso -3
1--1.574 Å20 Å20 Å2
2---1.386 Å20 Å2
3---2.959 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5089 850 70 838 6847
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.3341.5
X-RAY DIFFRACTIONc_scbond_it2.1012
X-RAY DIFFRACTIONc_mcangle_it2.1422
X-RAY DIFFRACTIONc_scangle_it3.0852.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4r517kt1.par

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