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- PDB-5ca7: Human DNA polymerase lambda- MgdGTP binary and complex with 6 pai... -

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Basic information

Entry
Database: PDB / ID: 5ca7
TitleHuman DNA polymerase lambda- MgdGTP 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 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'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / DNA / DNA polymerase lambda
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.522 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
DepositionJun 29, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Database references
Revision 1.2Feb 19, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)78,9427
Polymers78,3154
Non-polymers6283
Water3,315184
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 area2770 Å2
ΔGint-11 kcal/mol
Surface area13010 Å2
MethodPISA
2
A: DNA polymerase lambda
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9764
Polymers37,3491
Non-polymers6283
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-20 kcal/mol
Surface area12540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.113, 84.113, 399.442
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 , 4 types, 187 molecules

#4: Chemical ChemComp-DGT / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / Deoxyguanosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.6 Å3/Da / Density % sol: 52.77 %
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: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Dec 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.52→30 Å / Num. obs: 29246 / % possible obs: 98.3 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.039 / Rrim(I) all: 0.1 / Χ2: 1 / Net I/av σ(I): 19.5 / Net I/σ(I): 9.8 / Num. measured all: 195094
Reflection shell

Χ2: 1 / Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) all% possible all
2.52-2.616.60.69427300.8490.2880.75294.6
2.61-2.716.70.52528620.920.2160.56998.8
2.71-2.846.80.37228350.9490.1520.40298.6
2.84-2.996.90.25428710.9790.1030.27599
2.99-3.176.90.17428860.9860.0710.18898.9
3.17-3.4270.12428990.9940.0510.13599
3.42-3.766.90.08829320.9960.0360.09699.3
3.76-4.316.70.06129780.9970.0250.06699
4.31-5.426.40.05530150.9970.0240.0698.6
5.42-305.90.04232380.9980.0190.04797.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XSL

1xsl


Resolution: 2.522→28.311 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2462 1999 6.84 %
Rwork0.2085 --
obs0.211 29218 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.522→28.311 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3856 243 37 184 4320
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024245
X-RAY DIFFRACTIONf_angle_d0.65787
X-RAY DIFFRACTIONf_dihedral_angle_d15.9091592
X-RAY DIFFRACTIONf_chiral_restr0.022625
X-RAY DIFFRACTIONf_plane_restr0.002711
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5217-2.58470.33061370.26741862X-RAY DIFFRACTION98
2.5847-2.65460.29661390.24941890X-RAY DIFFRACTION99
2.6546-2.73260.30851380.24291887X-RAY DIFFRACTION99
2.7326-2.82070.30361410.251911X-RAY DIFFRACTION99
2.8207-2.92150.31271380.24741891X-RAY DIFFRACTION99
2.9215-3.03830.28141410.25371917X-RAY DIFFRACTION99
3.0383-3.17640.29961390.24261897X-RAY DIFFRACTION99
3.1764-3.34360.2711420.24221929X-RAY DIFFRACTION99
3.3436-3.55270.27081430.21941938X-RAY DIFFRACTION100
3.5527-3.82640.23181450.20221969X-RAY DIFFRACTION100
3.8264-4.21040.22681440.18381963X-RAY DIFFRACTION99
4.2104-4.81710.20311440.17711961X-RAY DIFFRACTION99
4.8171-6.05920.22221500.19392048X-RAY DIFFRACTION100
6.0592-28.31260.20551580.1792156X-RAY DIFFRACTION98

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