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- PDB-3hx0: ternary complex of L277A, H511A, R514 mutant pol lambda bound to ... -

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Basic information

Entry
Database: PDB / ID: 3hx0
Titleternary complex of L277A, H511A, R514 mutant pol lambda bound to a 2 nucleotide gapped DNA substrate with a scrunched dA
Components
  • 5'-D(*CP*AP*GP*TP*AP*T)-3'
  • 5'-D(*CP*GP*GP*CP*AP*AP*AP*TP*AP*CP*TP*G)-3'
  • 5'-D(P*GP*CP*CP*G)-3'
  • DNA polymerase lambda
KeywordsTRANSFERASE/DNA / scrunch / X-family / polymerase lambda / DNA damage / DNA repair / DNA replication / DNA synthesis / DNA-binding / DNA-directed DNA polymerase / Lyase / Manganese / Metal-binding / Nucleotidyltransferase / Nucleus / Phosphoprotein / Polymorphism / Transferase / 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 replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / 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 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsGarcia-Diaz, M. / Bebenek, K. / Larrea, A.A. / Havener, J.M. / Perera, L. / Krahn, J.M. / Pedersen, L.C. / Ramsden, D.A. / Kunkel, T.A.
CitationJournal: To be Published
Title: Scrunching During DNA Repair Synthesis
Authors: Garcia-Diaz, M. / Bebenek, K. / Larrea, A.A. / Havener, J.M. / Perera, L. / Krahn, J.M. / Pedersen, L.C. / Ramsden, D.A. / Kunkel, T.A.
History
DepositionJun 19, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations ...Database references / Derived calculations / Source and taxonomy / Structure summary
Category: database_2 / entity ...database_2 / entity / entity_name_com / entity_src_gen / pdbx_entity_src_syn / pdbx_struct_conn_angle / struct_conn / struct_ref / struct_ref_seq / 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 / _entity.pdbx_ec / _entity_name_com.name / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_seq_type / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _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_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.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 / _struct_ref_seq_dif.align_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase lambda
B: 5'-D(*CP*GP*GP*CP*AP*AP*AP*TP*AP*CP*TP*G)-3'
C: 5'-D(*CP*AP*GP*TP*AP*T)-3'
D: 5'-D(P*GP*CP*CP*G)-3'
F: DNA polymerase lambda
G: 5'-D(*CP*GP*GP*CP*AP*AP*AP*TP*AP*CP*TP*G)-3'
H: 5'-D(*CP*AP*GP*TP*AP*T)-3'
I: 5'-D(P*GP*CP*CP*G)-3'
K: DNA polymerase lambda
L: 5'-D(*CP*GP*GP*CP*AP*AP*AP*TP*AP*CP*TP*G)-3'
M: 5'-D(*CP*AP*GP*TP*AP*T)-3'
N: 5'-D(P*GP*CP*CP*G)-3'
P: DNA polymerase lambda
Q: 5'-D(*CP*GP*GP*CP*AP*AP*AP*TP*AP*CP*TP*G)-3'
R: 5'-D(*CP*AP*GP*TP*AP*T)-3'
S: 5'-D(P*GP*CP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,77229
Polymers175,69616
Non-polymers2,07713
Water63135
1
A: DNA polymerase lambda
B: 5'-D(*CP*GP*GP*CP*AP*AP*AP*TP*AP*CP*TP*G)-3'
C: 5'-D(*CP*AP*GP*TP*AP*T)-3'
D: 5'-D(P*GP*CP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4146
Polymers43,9244
Non-polymers4902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5210 Å2
ΔGint-23 kcal/mol
Surface area18240 Å2
MethodPISA
2
F: DNA polymerase lambda
G: 5'-D(*CP*GP*GP*CP*AP*AP*AP*TP*AP*CP*TP*G)-3'
H: 5'-D(*CP*AP*GP*TP*AP*T)-3'
I: 5'-D(P*GP*CP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4377
Polymers43,9244
Non-polymers5133
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5370 Å2
ΔGint-38 kcal/mol
Surface area18030 Å2
MethodPISA
3
K: DNA polymerase lambda
L: 5'-D(*CP*GP*GP*CP*AP*AP*AP*TP*AP*CP*TP*G)-3'
M: 5'-D(*CP*AP*GP*TP*AP*T)-3'
N: 5'-D(P*GP*CP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4608
Polymers43,9244
Non-polymers5364
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-52 kcal/mol
Surface area18730 Å2
MethodPISA
4
P: DNA polymerase lambda
Q: 5'-D(*CP*GP*GP*CP*AP*AP*AP*TP*AP*CP*TP*G)-3'
R: 5'-D(*CP*AP*GP*TP*AP*T)-3'
S: 5'-D(P*GP*CP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4608
Polymers43,9244
Non-polymers5364
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-51 kcal/mol
Surface area18750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.179, 131.912, 280.412
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsProtein functions as monomer

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Components

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Protein , 1 types, 4 molecules AFKP

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


Mass: 37252.426 Da / Num. of mol.: 4 / Fragment: UNP residues 242-575, Catalytic domain / Mutation: L277A, H511A, R514A ,C543A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLL / Plasmid: PET-22B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL
References: UniProt: Q9UGP5, DNA-directed DNA polymerase, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases

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DNA chain , 3 types, 12 molecules BGLQCHMRDINS

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


Mass: 3671.418 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: synthesized template
#3: DNA chain
5'-D(*CP*AP*GP*TP*AP*T)-3'


Mass: 1808.229 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: synthesized primer
#4: DNA chain
5'-D(P*GP*CP*CP*G)-3'


Mass: 1191.818 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: synthesized downstream primer

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Non-polymers , 4 types, 48 molecules

#5: Chemical
ChemComp-D3T / 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE


Type: DNA OH 3 prime terminus / Mass: 466.169 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N2O13P3
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#7: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 3.27 Å3/Da / Density % sol: 62.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 5% 2-propanol, 25mM ammonium acetate, 15mM magnesium acetate, 100mM cacodylic acid., pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9999 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 17, 2008
RadiationMonochromator: sagitally focused Si-220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 44203 / Num. obs: 44203 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 110.1 Å2 / Rsym value: 0.107 / Net I/σ(I): 9.4
Reflection shellResolution: 3→3.1 Å / Redundancy: 8.3 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 4339 / Rsym value: 0.745 / % possible all: 99.5

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3HWT

3hwt


Resolution: 3→39.11 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 67836.03 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.268 2145 5 %RANDOM
Rwork0.223 ---
obs0.223 42765 94.5 %-
all-44203 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.1112 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 88.2 Å2
Baniso -1Baniso -2Baniso -3
1--7.89 Å20 Å20 Å2
2--13.72 Å20 Å2
3----5.82 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.66 Å0.58 Å
Refinement stepCycle: LAST / Resolution: 3→39.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10006 1784 121 35 11946
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.003
X-RAY DIFFRACTIONc_angle_deg0.8
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_improper_angle_d0.69
X-RAY DIFFRACTIONc_mcbond_it1.231.5
X-RAY DIFFRACTIONc_mcangle_it2.182
X-RAY DIFFRACTIONc_scbond_it5.82
X-RAY DIFFRACTIONc_scangle_it7.492.5
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.379 249 5.3 %
Rwork0.35 4459 -
obs--61.7 %
Xplor fileSerial no: 1 / Param file: all.par / Topol file: all.top

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