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- PDB-4xq8: Human DNA polymerase lambda- MgdATP binary complex and complex wi... -

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Basic information

Entry
Database: PDB / ID: 4xq8
TitleHuman DNA polymerase lambda- MgdATP binary complex and complex with 6 paired DNA
Components
  • DNA (5'-D(*CP*AP*GP*TP*AP*C)-3')
  • DNA (5'-D(P*GP*TP*AP*CP*TP*G)-3')
  • DNA polymerase lambda
KeywordsTRANSFERASE/DNA / complex / MgdATP / 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, 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 ...Beta Polymerase; domain 3 / DNA polymerase, thumb domain / DNA polymerase family X, beta-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'-DEOXYADENOSINE 5'-TRIPHOSPHATE / DNA / DNA polymerase lambda
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.798 Å
AuthorsTsai, M.D. / Liu, M.S.
CitationJournal: J.Am.Chem.Soc. / Year: 2016
Title: Structural Mechanism for the Fidelity Modulation of DNA Polymerase lambda
Authors: Liu, M.S. / Tsai, H.Y. / Liu, X.X. / Ho, M.C. / Wu, W.J. / Tsai, M.D.
History
DepositionJan 19, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Database references
Revision 1.2Nov 8, 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_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA polymerase lambda
A: DNA polymerase lambda
P: DNA (5'-D(*CP*AP*GP*TP*AP*C)-3')
T: DNA (5'-D(P*GP*TP*AP*CP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,8306
Polymers78,3154
Non-polymers5152
Water1,78399
1
B: DNA polymerase lambda
P: DNA (5'-D(*CP*AP*GP*TP*AP*C)-3')
T: DNA (5'-D(P*GP*TP*AP*CP*TP*G)-3')


Theoretical massNumber of molelcules
Total (without water)40,9663
Polymers40,9663
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-10 kcal/mol
Surface area12860 Å2
MethodPISA
2
A: DNA polymerase lambda
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8643
Polymers37,3491
Non-polymers5152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area740 Å2
ΔGint-8 kcal/mol
Surface area12470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.743, 83.743, 398.746
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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Protein , 1 types, 2 molecules BA

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


Mass: 37348.559 Da / Num. of mol.: 2 / Fragment: UNP residues 242-575
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

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DNA chain , 2 types, 2 molecules PT

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


Mass: 1793.219 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*GP*TP*AP*CP*TP*G)-3')


Mass: 1824.228 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 101 molecules

#4: Chemical ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / Deoxyadenosine triphosphate


Mass: 491.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.58 Å3/Da / Density % sol: 52.27 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: 0.1 M Lithium Sulfate monohydrate, 0.1 M HEPES-Sodium, 0.1 M Potassium Sodium Tartrate

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.798→30 Å / Num. obs: 21679 / % possible obs: 100 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.031 / Rrim(I) all: 0.089 / Χ2: 0.916 / Net I/av σ(I): 24.324 / Net I/σ(I): 9.5 / Num. measured all: 178549
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.8-2.97.80.49120700.9020.1870.5260.895100
2.9-3.028.50.35521050.9630.1290.3780.886100
3.02-3.158.60.26720970.9760.0960.2850.913100
3.15-3.328.60.17621280.9890.0640.1880.917100
3.32-3.538.50.10821230.9960.0390.1150.9100
3.53-3.88.50.07921470.9970.0280.0840.874100
3.8-4.188.40.05421500.9980.0190.0570.801100
4.18-4.788.20.04721660.9980.0170.0510.84799.9
4.78-6.0280.06522620.9970.0240.0691.386100
6.02-307.40.026243110.010.0280.73599.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4W5D

4w5d
PDB Unreleased entry


Resolution: 2.798→27.411 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2399 1652 9.22 %
Rwork0.1817 --
obs0.187 17909 92.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.798→27.411 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3863 243 31 99 4236
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094247
X-RAY DIFFRACTIONf_angle_d1.1835790
X-RAY DIFFRACTIONf_dihedral_angle_d17.6171607
X-RAY DIFFRACTIONf_chiral_restr0.043627
X-RAY DIFFRACTIONf_plane_restr0.006713
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7981-2.83810.2752880.2513890X-RAY DIFFRACTION62
2.8381-2.88040.3254980.241985X-RAY DIFFRACTION66
2.8804-2.92540.25311040.22331022X-RAY DIFFRACTION71
2.9254-2.97330.30631100.23921093X-RAY DIFFRACTION74
2.9733-3.02450.26881120.23781189X-RAY DIFFRACTION81
3.0245-3.07940.32951240.24421243X-RAY DIFFRACTION86
3.0794-3.13850.35551350.2561330X-RAY DIFFRACTION92
3.1385-3.20250.34931490.23581444X-RAY DIFFRACTION98
3.2025-3.2720.27231480.2351432X-RAY DIFFRACTION100
3.272-3.3480.30421500.2151493X-RAY DIFFRACTION100
3.348-3.43160.25421490.21141431X-RAY DIFFRACTION100
3.4316-3.52420.2451500.20321462X-RAY DIFFRACTION100
3.5242-3.62770.27851570.18761491X-RAY DIFFRACTION100
3.6277-3.74450.27181410.18811405X-RAY DIFFRACTION100
3.7445-3.8780.22971540.17741471X-RAY DIFFRACTION100
3.878-4.03280.2321520.16611466X-RAY DIFFRACTION100
4.0328-4.21570.19871500.15041453X-RAY DIFFRACTION100
4.2157-4.43710.2051490.15451463X-RAY DIFFRACTION100
4.4371-4.71370.24741450.14751456X-RAY DIFFRACTION100
4.7137-5.07560.20291480.13751440X-RAY DIFFRACTION100
5.0756-5.58250.19911530.16371494X-RAY DIFFRACTION100
5.5825-6.38140.18011420.16171441X-RAY DIFFRACTION100
6.3814-8.00650.19951450.15681459X-RAY DIFFRACTION100
8.0065-27.41260.18751500.15361461X-RAY DIFFRACTION99

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