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- PDB-4fo6: Crystal structure of the pre-catalytic ternary complex of polymer... -

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Basic information

Entry
Database: PDB / ID: 4fo6
TitleCrystal structure of the pre-catalytic ternary complex of polymerase lambda with a dATP analog opposite a templating T and an rCMP at the primer terminus.
Components
  • 5'-D(*CP*AP*GP*TP*AP)-R(P*C)-3'
  • 5'-D(*CP*GP*GP*CP*TP*GP*TP*AP*CP*TP*G)-3'
  • 5'-D(P*CP*AP*GP*TP*A)-3'
  • 5'-D(P*GP*CP*CP*G)-3'
  • 5'-D(P*TP*AP*CP*TP*G)-3'
  • DNA polymerase lambda
KeywordsTRANSFERASE / LYASE/DNA / DNA polymerase / 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-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
Chem-F2A / : / DNA / DNA (> 10) / DNA/RNA hybrid / DNA polymerase lambda
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.007 Å
AuthorsGosavi, R.A. / Moon, A.F. / Kunkel, T.A. / Pedersen, L.C. / Bebenek, K.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: The catalytic cycle for ribonucleotide incorporation by human DNA Pol lambda
Authors: Gosavi, R.A. / Moon, A.F. / Kunkel, T.A. / Pedersen, L.C. / Bebenek, K.
History
DepositionJun 20, 2012Deposition site: RCSB / Processing site: RCSB
SupersessionJul 11, 2012ID: 3UQ1
Revision 1.0Jul 11, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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 / database_2 / pdbx_initial_refinement_model / 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_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.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: 5'-D(*CP*GP*GP*CP*TP*GP*TP*AP*CP*TP*G)-3'
P: 5'-D(*CP*AP*GP*TP*AP)-R(P*C)-3'
D: 5'-D(P*GP*CP*CP*G)-3'
H: 5'-D(P*TP*AP*CP*TP*G)-3'
I: 5'-D(P*CP*AP*GP*TP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,71912
Polymers46,0696
Non-polymers6506
Water3,819212
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.780, 63.655, 141.470
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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DNA chain , 4 types, 4 molecules TDHI

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


Mass: 3365.196 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: DNA chain 5'-D(P*GP*CP*CP*G)-3'


Mass: 1191.818 Da / Num. of mol.: 1 / Source method: obtained synthetically
#5: DNA chain 5'-D(P*TP*AP*CP*TP*G)-3'


Mass: 1495.023 Da / Num. of mol.: 1 / Source method: obtained synthetically
#6: DNA chain 5'-D(P*CP*AP*GP*TP*A)-3'


Mass: 1504.037 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source

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Protein / DNA/RNA hybrid , 2 types, 2 molecules AP

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


Mass: 36703.977 Da / Num. of mol.: 1 / Fragment: Loop mutant of DNA polymerase lambda / Mutation: SQEENGQQQ to KGET
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLL / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UGP5, DNA-directed DNA polymerase, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases
#3: DNA/RNA hybrid 5'-D(*CP*AP*GP*TP*AP)-R(P*C)-3'


Mass: 1809.219 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 6 types, 218 molecules

#7: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#9: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#10: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#11: Chemical ChemComp-F2A / 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]adenosine


Mass: 489.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O11P3
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsAUTHORS STATE THAT THIS IS A DELETION-SUBSTITUTION MUTANT, WITH RESIDUES SQEENGQQQ IN THE WILDTYPE ...AUTHORS STATE THAT THIS IS A DELETION-SUBSTITUTION MUTANT, WITH RESIDUES SQEENGQQQ IN THE WILDTYPE SUBSTITUTED BY RESIDUES KGET. HOWEVER, THE RESIDUE NUMBERING WAS KEPT CONSISTENT WITH THE WT PROTEIN.

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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: 2.73 Å3/Da / Density % sol: 54.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 50mM MES pH 6.5, 9%(v/v) PEG400, 100mM KCL, 10mM MGCL2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. all: 34370 / Num. obs: 32824 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 28.84 Å2
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.9 / Rsym value: 0.297 / % possible all: 78.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.2_868)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 3MGI

3mgi


Resolution: 2.007→24.027 Å / SU ML: 0.56 / σ(F): 1.35 / Phase error: 23.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2306 1603 4.9 %R free flags used from 3MGI
Rwork0.1898 ---
all0.1918 ---
obs0.1918 32824 95.05 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.91 Å2 / ksol: 0.381 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.5007 Å20 Å2-0 Å2
2--10.6081 Å2-0 Å2
3----3.221 Å2
Refinement stepCycle: LAST / Resolution: 2.007→24.027 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2383 626 35 212 3256
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113191
X-RAY DIFFRACTIONf_angle_d1.1594471
X-RAY DIFFRACTIONf_dihedral_angle_d11.139886
X-RAY DIFFRACTIONf_chiral_restr0.071501
X-RAY DIFFRACTIONf_plane_restr0.005453
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0073-2.0720.24191070.22742203X-RAY DIFFRACTION75
2.072-2.1460.2761290.23152465X-RAY DIFFRACTION84
2.146-2.23190.28391420.23132717X-RAY DIFFRACTION93
2.2319-2.33340.24811470.21242851X-RAY DIFFRACTION97
2.3334-2.45630.25091480.20172915X-RAY DIFFRACTION99
2.4563-2.610.25361520.20342922X-RAY DIFFRACTION99
2.61-2.81130.28291560.20132962X-RAY DIFFRACTION100
2.8113-3.09370.28541630.20642971X-RAY DIFFRACTION100
3.0937-3.54010.21671480.18163008X-RAY DIFFRACTION100
3.5401-4.45550.18961530.15433018X-RAY DIFFRACTION100
4.4555-24.02850.20111580.18833107X-RAY DIFFRACTION98

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