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- PDB-3pml: crystal structure of a polymerase lambda variant with a dGTP anal... -

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Basic information

Entry
Database: PDB / ID: 3pml
Titlecrystal structure of a polymerase lambda variant with a dGTP 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
KeywordsLYASE / TRANSFERASE/DNA / PROTEIN-DNA COMPLEX / TRANSFERASE / DNA / 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 / 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, 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-1GC / DNA / DNA (> 10) / DNA polymerase lambda
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.6 Å
AuthorsBebenek, K. / Pedersen, L.C. / Kunkel, T.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Replication infidelity via a mismatch with Watson-Crick geometry.
Authors: Bebenek, K. / Pedersen, L.C. / Kunkel, T.A.
History
DepositionNov 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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.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.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
Remark 999Author states that polymerase lambda loop residues from 463 to 471 (SQEENGQQQ) are replaced by residues "KGET"

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase lambda
B: DNA polymerase lambda
C: 5'-D(*CP*GP*GP*CP*TP*GP*TP*AP*CP*TP*G)-3'
D: 5'-D(P*GP*CP*CP*G)-3'
E: 5'-D(*CP*GP*GP*CP*TP*GP*TP*AP*CP*TP*G)-3'
F: 5'-D(*CP*AP*GP*TP*AP*C)-3'
G: 5'-D(P*GP*CP*CP*G)-3'
H: 5'-D(*CP*AP*GP*TP*AP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,34917
Polymers86,1738
Non-polymers1,1779
Water3,027168
1
A: DNA polymerase lambda
C: 5'-D(*CP*GP*GP*CP*TP*GP*TP*AP*CP*TP*G)-3'
D: 5'-D(P*GP*CP*CP*G)-3'
H: 5'-D(*CP*AP*GP*TP*AP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6638
Polymers43,0864
Non-polymers5774
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-57 kcal/mol
Surface area17930 Å2
MethodPISA
2
B: DNA polymerase lambda
E: 5'-D(*CP*GP*GP*CP*TP*GP*TP*AP*CP*TP*G)-3'
F: 5'-D(*CP*AP*GP*TP*AP*C)-3'
G: 5'-D(P*GP*CP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6869
Polymers43,0864
Non-polymers6005
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-68 kcal/mol
Surface area18440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.038, 191.570, 59.084
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 beta-2 / Pol beta2 / DNA polymerase kappa


Mass: 36736.039 Da / Num. of mol.: 2 / Fragment: UNP residues 242-575
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: 562 / Gene: POLL / Plasmid: PET22 / 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, 6 molecules CEDGFH

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


Mass: 3365.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Templating strand DNA
#3: DNA chain 5'-D(P*GP*CP*CP*G)-3'


Mass: 1191.818 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Primer strand DNA
#4: DNA chain 5'-D(*CP*AP*GP*TP*AP*C)-3'


Mass: 1793.219 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Downstream strand DNA

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Non-polymers , 4 types, 177 molecules

#5: Chemical ChemComp-1GC / 2'-deoxy-5'-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]guanosine


Mass: 505.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O12P3
#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.: 3 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.8 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: .1M NaCl, 0.1M Hepes pH 7.5 and 10%PEG4000, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 18, 2008
RadiationMonochromator: Double Crystal monochromator Si-220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 34636 / Num. obs: 34636 / % possible obs: 99.9 % / Observed criterion σ(F): 244249 / Observed criterion σ(I): 244249 / Redundancy: 7.1 % / Biso Wilson estimate: 53.1 Å2 / Rsym value: 0.07 / Net I/σ(I): 10.6
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 7 % / Rmerge(I) obs: 0.572 / Mean I/σ(I) obs: 3.5 / Num. unique all: 3424 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MAR345data collection
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
CNS1.1phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.6→25.02 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 72742.99 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.271 1611 4.9 %RANDOM
Rwork0.233 ---
obs0.233 33162 95.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 20.9968 Å2 / ksol: 0.275127 e/Å3
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.55 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.6→25.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5018 850 69 168 6105
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_improper_angle_d0.95
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.482 238 4.8 %
Rwork0.376 4716 -
obs--87.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1all.parprotein.top
X-RAY DIFFRACTION2dna-rna.top
X-RAY DIFFRACTION3water.top
X-RAY DIFFRACTION4nucleic_compounds.top
X-RAY DIFFRACTION5ion.top

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