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- PDB-3c5f: Structure of a binary complex of the R517A Pol lambda mutant -

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Basic information

Entry
Database: PDB / ID: 3c5f
TitleStructure of a binary complex of the R517A Pol lambda mutant
Components
  • DNA (5'-D(*DCP*DAP*DGP*DTP*DAP*DC)-3')
  • DNA (5'-D(*DCP*DGP*DGP*DCP*DCP*DGP*DTP*DAP*DCP*DTP*DG)-3')
  • DNA (5'-D(P*DGP*DCP*DCP*DG)-3')
  • DNA polymerase lambda
KeywordsTransferase / 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 / Polymorphism / Lyase-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 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 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 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
DNA / DNA (> 10) / DNA polymerase lambda
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.25 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 1.0Sep 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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_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_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_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
T: DNA (5'-D(*DCP*DGP*DGP*DCP*DCP*DGP*DTP*DAP*DCP*DTP*DG)-3')
P: DNA (5'-D(*DCP*DAP*DGP*DTP*DAP*DC)-3')
D: DNA (5'-D(P*DGP*DCP*DCP*DG)-3')
U: DNA (5'-D(*DCP*DGP*DGP*DCP*DCP*DGP*DTP*DAP*DCP*DTP*DG)-3')
Q: DNA (5'-D(*DCP*DAP*DGP*DTP*DAP*DC)-3')
E: DNA (5'-D(P*DGP*DCP*DCP*DG)-3')
A: DNA polymerase lambda
B: DNA polymerase lambda
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,59614
Polymers87,4588
Non-polymers1386
Water11,512639
1
T: DNA (5'-D(*DCP*DGP*DGP*DCP*DCP*DGP*DTP*DAP*DCP*DTP*DG)-3')
P: DNA (5'-D(*DCP*DAP*DGP*DTP*DAP*DC)-3')
D: DNA (5'-D(P*DGP*DCP*DCP*DG)-3')
A: DNA polymerase lambda
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7987
Polymers43,7294
Non-polymers693
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
U: DNA (5'-D(*DCP*DGP*DGP*DCP*DCP*DGP*DTP*DAP*DCP*DTP*DG)-3')
Q: DNA (5'-D(*DCP*DAP*DGP*DTP*DAP*DC)-3')
E: DNA (5'-D(P*DGP*DCP*DCP*DG)-3')
B: DNA polymerase lambda
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7987
Polymers43,7294
Non-polymers693
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.237, 151.884, 85.635
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Number of models2

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Components

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DNA chain , 3 types, 6 molecules TUPQDE

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


Mass: 3350.185 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Template
#2: DNA chain DNA (5'-D(*DCP*DAP*DGP*DTP*DAP*DC)-3')


Mass: 1793.219 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Primer
#3: 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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Protein , 1 types, 2 molecules AB

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


Mass: 37393.633 Da / Num. of mol.: 2 / Fragment: DNA binding region / Mutation: R517A
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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Non-polymers , 2 types, 645 molecules

#5: Chemical
ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 639 / 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: 3.5 Å3/Da / Density % sol: 64.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M ammonium acetate, 100 mM Hepes, pH 7 and 10% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1ammonium acetate11
2Hepes11
3PEG 400011
4ammonium acetate12
5Hepes12
6PEG 400012

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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: Dec 21, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 56848 / % possible obs: 96.8 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.113 / Χ2: 1.043 / Net I/σ(I): 11.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.25-2.334.40.60652921.10291.5
2.33-2.424.50.49353421.08792.5
2.42-2.534.60.42154581.09493.8
2.53-2.674.80.33255301.10295.1
2.67-2.834.90.2656371.197.1
2.83-3.055.20.19657691.06298.8
3.05-3.365.60.13458341.05299.6
3.36-3.856.40.10258620.97399.8
3.85-4.857.50.08659470.98599.9
4.85-507.80.06661771.00499.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.004data extraction
HKL-2000data collection
CNSphasing
RefinementResolution: 2.25→50 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.263 2548 4.3 %
Rwork0.224 --
obs-50327 85.2 %
Solvent computationBsol: 33.712 Å2
Displacement parametersBiso mean: 32.983 Å2
Baniso -1Baniso -2Baniso -3
1--1.597 Å20 Å20 Å2
2---2.893 Å20 Å2
3---4.49 Å2
Refinement stepCycle: LAST / Resolution: 2.25→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5092 848 6 639 6585
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.3711.5
X-RAY DIFFRACTIONc_scbond_it1.9622
X-RAY DIFFRACTIONc_mcangle_it2.1932
X-RAY DIFFRACTIONc_scangle_it2.9562.5
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 DIFFRACTION4R517Agap.par

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