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- PDB-1xsl: Crystal Structure of human DNA polymerase lambda in complex with ... -

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Basic information

Entry
Database: PDB / ID: 1xsl
TitleCrystal Structure of human DNA polymerase lambda in complex with a one nucleotide DNA gap
Components
  • 5'-D(*CP*GP*GP*CP*AP*GP*CP*GP*CP*AP*C)-3'
  • 5'-D(*GP*TP*GP*CP*GP*C)-3'
  • 5'-D(P*GP*CP*CP*G)-3'
  • DNA polymerase lambda
KeywordsTRANSFERASE/DNA / DNA POLYMERASE LAMBDA / Protein-DNA complex / Helix-hairpin-helix / 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
CACODYLATE ION / DNA / DNA (> 10) / DNA polymerase lambda
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGarcia-Diaz, M. / Bebenek, K. / Krahn, J.M. / Kunkel, T.A. / Pedersen, L.C.
Citation
Journal: Nat.Struct.Mol.Biol. / Year: 2005
Title: A closed conformation for the Pol lambda catalytic cycle.
Authors: Garcia-Diaz, M. / Bebenek, K. / Krahn, J.M. / Kunkel, T.A. / Pedersen, L.C.
#1: Journal: Mol.Cell / Year: 2004
Title: A Structural Solution for the DNA Polymerase-lambda Dependent Repair of DNA Gaps with Minimal Homology
Authors: Garcia-Diaz, M. / Bebenek, K. / Krahn, J.M. / Blanco, L. / Kunkel, T.A. / Pedersen, L.C.
#2: Journal: J.Biol.Chem. / Year: 2002
Title: DNA polymerase lambda, a novel DNA repair enzyme in human cells
Authors: Garcia-Diaz, M. / Bebenek, K. / Sabariegos, R. / Dominguez, O. / Rodriguez, J. / Kirchhoff, T. / Garcia-Palomero, E. / Picher, A.J. / Juarez, R. / Ruiz, J.F. / Kunkel, T.A. / Blanco, L.
#3: Journal: J.Biol.Chem. / Year: 2003
Title: The frameshift Infidelity of human DNA polymerase lambda. Implications for function.
Authors: Bebenek, K. / Garcia-Diaz, K. / Blanco, L. / Kunkel, T.A.
#4: Journal: J.Biol.Chem. / Year: 2001
Title: Identification of an intrinsic 5'-deoxyribose-5-phosphate lyase activity in human DNA polymerase lambda: a possible role in Base Excision Repair
Authors: Garcia-Diaz, M. / Bebenek, K. / Kunkel, T.A. / Blanco, L.
History
DepositionOct 19, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)175,71226
Polymers175,36416
Non-polymers34810
Water15,187843
1
B: 5'-D(*CP*GP*GP*CP*AP*GP*CP*GP*CP*AP*C)-3'
C: 5'-D(*GP*TP*GP*CP*GP*C)-3'
D: 5'-D(P*GP*CP*CP*G)-3'
A: DNA polymerase lambda
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0257
Polymers43,8414
Non-polymers1843
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: 5'-D(*CP*GP*GP*CP*AP*GP*CP*GP*CP*AP*C)-3'
G: 5'-D(*GP*TP*GP*CP*GP*C)-3'
H: 5'-D(P*GP*CP*CP*G)-3'
E: DNA polymerase lambda
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9137
Polymers43,8414
Non-polymers723
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
J: 5'-D(*CP*GP*GP*CP*AP*GP*CP*GP*CP*AP*C)-3'
K: 5'-D(*GP*TP*GP*CP*GP*C)-3'
L: 5'-D(P*GP*CP*CP*G)-3'
I: DNA polymerase lambda
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8876
Polymers43,8414
Non-polymers462
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
N: 5'-D(*CP*GP*GP*CP*AP*GP*CP*GP*CP*AP*C)-3'
O: 5'-D(*GP*TP*GP*CP*GP*C)-3'
P: 5'-D(P*GP*CP*CP*G)-3'
M: DNA polymerase lambda
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8876
Polymers43,8414
Non-polymers462
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)191.504, 98.812, 104.519
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11E-1066-

HOH

DetailsThe protein is a monomer thus the asymmetric unit represents four biological units

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Components

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DNA chain , 3 types, 12 molecules BFJNCGKODHLP

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


Mass: 3344.188 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: Template DNA
#2: DNA chain
5'-D(*GP*TP*GP*CP*GP*C)-3'


Mass: 1825.216 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: Primer DNA
#3: DNA chain
5'-D(P*GP*CP*CP*G)-3'


Mass: 1191.818 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: Downstream Primer DNA

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Protein , 1 types, 4 molecules AEIM

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


Mass: 37479.750 Da / Num. of mol.: 4 / Fragment: 39 kDa catalytic C-terminal domain
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

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Non-polymers , 4 types, 853 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate / Cacodylic acid


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#7: Chemical
ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 843 / 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: 2.7 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: MPD, Cacodylate, sodium chloride, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2CacodylateCacodylic acid11
3sodium chloride11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 16, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 88074 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 29 Å2 / Rsym value: 0.145 / Net I/σ(I): 8.17
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.1 % / % possible all: 91.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→28.47 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 447347.11 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.252 4166 5 %RANDOM
Rwork0.207 ---
all0.209 86802 --
obs0.207 82636 93.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.8868 Å2 / ksol: 0.309474 e/Å3
Displacement parametersBiso mean: 42.6 Å2
Baniso -1Baniso -2Baniso -3
1-3.29 Å20 Å20 Å2
2---3.54 Å20 Å2
3---0.25 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.3→28.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10181 1704 14 843 12742
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.94
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.261.5
X-RAY DIFFRACTIONc_mcangle_it2.042
X-RAY DIFFRACTIONc_scbond_it2.842
X-RAY DIFFRACTIONc_scangle_it4.392.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.327 553 4.6 %
Rwork0.274 11524 -
obs--82.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4GCMPD1.PARAMGCMPD1.TOP
X-RAY DIFFRACTION5ION.TOP

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