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- PDB-4xrh: Human DNA polymerase lambda- MgdTTP binary and complex with 6 pai... -

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Basic information

Entry
Database: PDB / ID: 4xrh
TitleHuman DNA polymerase lambda- MgdTTP binary 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 / DNA polymerase lambda / 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-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, 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 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
THYMIDINE-5'-TRIPHOSPHATE / DNA / DNA polymerase lambda
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsLiu, M.S. / Tsai, M.D.
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 21, 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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)79,0836
Polymers78,5774
Non-polymers5062
Water362
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)41,0973
Polymers41,0973
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-12 kcal/mol
Surface area12740 Å2
MethodPISA
2
A: DNA polymerase lambda
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9863
Polymers37,4801
Non-polymers5062
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area690 Å2
ΔGint-9 kcal/mol
Surface area12520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.083, 84.083, 397.760
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: 37479.750 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, 4 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-TTP / THYMIDINE-5'-TRIPHOSPHATE


Mass: 482.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N2O14P3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.58 Å3/Da / Density % sol: 52.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Lithium Sulfate monohydrate, 0.1M HEPES-Sodium, 0.1M 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: 3→30 Å / Num. obs: 17723 / % possible obs: 99.2 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.153 / Χ2: 1 / Net I/av σ(I): 11.261 / Net I/σ(I): 5.8 / Num. measured all: 98387
Reflection shell

Χ2: 1 / Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique all% possible all
3-3.115.40.701170599.8
3.11-3.235.60.552172999.5
3.23-3.385.80.371172099.7
3.38-3.565.90.267172199.7
3.56-3.785.90.215173899.7
3.78-4.075.70.147176399.5
4.07-4.485.60.098174999.3
4.48-5.125.40.1178499.2
5.12-6.445.30.101184399.1
6.44-304.90.045197197.2

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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: 1XSL

1xsl


Resolution: 3→29.375 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2514 1770 10.01 %
Rwork0.2179 --
obs0.2213 17683 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→29.375 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3856 243 30 2 4131
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034238
X-RAY DIFFRACTIONf_angle_d0.6655776
X-RAY DIFFRACTIONf_dihedral_angle_d16.6121605
X-RAY DIFFRACTIONf_chiral_restr0.026625
X-RAY DIFFRACTIONf_plane_restr0.003711
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0001-3.08110.32551300.28941170X-RAY DIFFRACTION100
3.0811-3.17170.35161310.2961180X-RAY DIFFRACTION100
3.1717-3.27390.33521330.28341187X-RAY DIFFRACTION100
3.2739-3.39080.29521320.26191199X-RAY DIFFRACTION100
3.3908-3.52630.29881340.24851205X-RAY DIFFRACTION100
3.5263-3.68650.25471320.23341184X-RAY DIFFRACTION100
3.6865-3.88050.26861350.22961211X-RAY DIFFRACTION100
3.8805-4.1230.22961340.19281206X-RAY DIFFRACTION100
4.123-4.44030.22991370.18551233X-RAY DIFFRACTION100
4.4403-4.88530.22741360.18511225X-RAY DIFFRACTION100
4.8853-5.5880.241400.19331258X-RAY DIFFRACTION100
5.588-7.02440.21491420.20721280X-RAY DIFFRACTION100
7.0244-29.37650.20791540.19391375X-RAY DIFFRACTION99

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