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- PDB-5cp2: Human DNA polymerase lambda L431A mutant- Apoenzyme and complex w... -

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Basic information

Entry
Database: PDB / ID: 5cp2
TitleHuman DNA polymerase lambda L431A mutant- Apoenzyme 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
DNA / DNA polymerase lambda
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 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
DepositionJul 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
A: DNA polymerase lambda
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')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,3265
Polymers78,2304
Non-polymers961
Water5,008278
1
A: DNA polymerase lambda
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4032
Polymers37,3061
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-13 kcal/mol
Surface area12390 Å2
MethodPISA
2
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)40,9243
Polymers40,9243
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-10 kcal/mol
Surface area12920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.876, 83.876, 396.363
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-791-

HOH

21A-807-

HOH

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Components

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


Mass: 37306.477 Da / Num. of mol.: 2 / Fragment: UNP residues 242-575 / Mutation: L431A
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
#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)
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 278 / Source method: isolated from a natural source / Formula: H2O
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: 2.57 Å3/Da / Density % sol: 52.19 %
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 / Type: OTHER / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.36→30 Å / Num. obs: 35440 / % possible obs: 99.8 % / Redundancy: 13.7 % / Biso Wilson estimate: 43.27 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 13
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.36-2.4314.20.5292814198.6
2.43-2.5114.20.4228871.001100
2.51-2.614.30.3228911.002100
2.6-2.714.20.23528841100
2.7-2.8214.10.17528811.003100
2.82-2.9714.10.12929071100
2.97-3.1613.80.10929171100
3.16-3.413.40.07929361100
3.4-3.7413.60.06329641100
3.74-4.2813.40.04430051100
4.28-5.3912.70.04530521100
5.39-3012.20.0263302199.3

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Processing

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

1xsl


Resolution: 2.36→25.95 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.238 3530 10 %
Rwork0.206 --
obs0.209 35302 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.36→25.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3800 243 5 278 4326
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054151
X-RAY DIFFRACTIONf_angle_d0.8235655
X-RAY DIFFRACTIONf_dihedral_angle_d15.0591554
X-RAY DIFFRACTIONf_chiral_restr0.03614
X-RAY DIFFRACTIONf_plane_restr0.005700
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.36-2.39230.26191370.23071238X-RAY DIFFRACTION100
2.3923-2.42650.30371370.24031228X-RAY DIFFRACTION100
2.4265-2.46270.28731380.23431256X-RAY DIFFRACTION100
2.4627-2.50110.32581360.23551218X-RAY DIFFRACTION100
2.5011-2.54210.28021410.23071261X-RAY DIFFRACTION100
2.5421-2.58590.24921340.2411211X-RAY DIFFRACTION100
2.5859-2.63280.28541400.2371262X-RAY DIFFRACTION100
2.6328-2.68340.28651370.21551233X-RAY DIFFRACTION100
2.6834-2.73820.31171380.24461239X-RAY DIFFRACTION100
2.7382-2.79760.3051420.21971273X-RAY DIFFRACTION100
2.7976-2.86260.26941340.22921212X-RAY DIFFRACTION100
2.8626-2.93410.28131400.21711258X-RAY DIFFRACTION100
2.9341-3.01330.24221410.23041267X-RAY DIFFRACTION100
3.0133-3.10190.24851390.22621256X-RAY DIFFRACTION100
3.1019-3.20180.28721390.24161251X-RAY DIFFRACTION100
3.2018-3.3160.2891410.23291273X-RAY DIFFRACTION100
3.316-3.44850.2461400.22361253X-RAY DIFFRACTION100
3.4485-3.60510.23271410.22341268X-RAY DIFFRACTION100
3.6051-3.79460.22571420.2021285X-RAY DIFFRACTION100
3.7946-4.03150.22041440.19181290X-RAY DIFFRACTION100
4.0315-4.34150.22841420.17611287X-RAY DIFFRACTION100
4.3415-4.77590.17471450.17251300X-RAY DIFFRACTION100
4.7759-5.46140.22471480.17761329X-RAY DIFFRACTION100
5.4614-6.85970.21951500.20111355X-RAY DIFFRACTION100
6.8597-25.95010.18581640.17881469X-RAY DIFFRACTION100

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