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- PDB-3upq: Crystal structure of the pre-catalytic ternary complex of polymer... -

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Basic information

Entry
Database: PDB / ID: 3upq
TitleCrystal structure of the pre-catalytic ternary complex of polymerase lambda with an rATP analog opposite a templating T.
Components
  • 5'-D(*CP*AP*GP*TP*AP*C)-3'
  • 5'-D(*CP*GP*GP*CP*TP*GP*TP*AP*CP*TP*G)-3'
  • 5'-D(P*GP*CP*CP*G)-3'
  • DNA polymerase lambda
KeywordsTRANSFERASE / LYASE/DNA / DNA / Polymerase / DNA polymerase lambda / ribonucleotide incorporation / 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
: / Chem-ZAN / DNA / DNA (> 10) / DNA polymerase lambda
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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
DepositionNov 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2012Group: Database references
Revision 1.2Sep 26, 2012Group: Database references
Revision 1.3Sep 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_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.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_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*C)-3'
D: 5'-D(P*GP*CP*CP*G)-3'
A: 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,16513
Polymers43,0864
Non-polymers1,0789
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-100 kcal/mol
Surface area16900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.975, 63.660, 139.970
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: 36736.039 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

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DNA chain , 3 types, 3 molecules TPD

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


Mass: 1793.219 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

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Non-polymers , 5 types, 264 molecules A

#5: Chemical ChemComp-ZAN / 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3
#6: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 2.89 Å3/Da / Density % sol: 57.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100mM Na HEPES pH 7.5, 1.0M lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 12, 2010
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 37285 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Rsym value: 0.058 / Net I/σ(I): 28.9
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 3.7 / Rsym value: 0.357 / % possible all: 98.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3MGI

3mgi


Resolution: 1.95→27.444 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 22.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2437 1787 4.89 %Used same free R flags as in PDB ENTRY 3MGI
Rwork0.2076 ---
all0.209 37285 --
obs0.2094 36538 98.02 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.188 Å2 / ksol: 0.331 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.8012 Å20 Å20 Å2
2--5.5762 Å20 Å2
3---0.225 Å2
Refinement stepCycle: LAST / Resolution: 1.95→27.444 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2289 425 55 255 3024
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012912
X-RAY DIFFRACTIONf_angle_d1.0694075
X-RAY DIFFRACTIONf_dihedral_angle_d12.836855
X-RAY DIFFRACTIONf_chiral_restr0.062450
X-RAY DIFFRACTIONf_plane_restr0.004441
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.00270.27131250.24012437X-RAY DIFFRACTION90
2.0027-2.06160.27411320.21712545X-RAY DIFFRACTION95
2.0616-2.12810.23051320.21412611X-RAY DIFFRACTION97
2.1281-2.20420.26391330.21042617X-RAY DIFFRACTION98
2.2042-2.29240.22941350.2222624X-RAY DIFFRACTION97
2.2924-2.39660.31681380.22412647X-RAY DIFFRACTION99
2.3966-2.52290.23791400.22022693X-RAY DIFFRACTION99
2.5229-2.68090.26491400.21772699X-RAY DIFFRACTION100
2.6809-2.88760.27191360.22682700X-RAY DIFFRACTION100
2.8876-3.17790.23131430.22522723X-RAY DIFFRACTION100
3.1779-3.63680.23551340.2072761X-RAY DIFFRACTION100
3.6368-4.57850.23711540.17722775X-RAY DIFFRACTION100
4.5785-27.4470.22251450.19952919X-RAY DIFFRACTION100

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