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- PDB-7m4d: DNA Polymerase Lambda, dCTP:At Ca2+ Ground State Ternary Complex -

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Basic information

Entry
Database: PDB / ID: 7m4d
TitleDNA Polymerase Lambda, dCTP:At Ca2+ Ground State Ternary Complex
Components
  • DNA (5'-D(*CP*AP*GP*TP*AP*C)-3')
  • DNA (5'-D(*CP*GP*GP*CP*AP*GP*TP*AP*CP*TP*G)-3')
  • DNA (5'-D(P*GP*CP*CP*G)-3')
  • DNA polymerase lambda
KeywordsREPLICATION / Time-Lapse Crystallography / Double Strand Break Repair / DNA Synthesis Fidelity
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 / nucleus / metal ion binding
Similarity search - Function
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, 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 / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Nucleotidyltransferase superfamily
Similarity search - Domain/homology
2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase lambda
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.817 Å
AuthorsJamsen, J.A. / Wilson, S.H.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)Z01-ES050158 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)Z01-ES050161 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1K99ES029572-01 United States
CitationJournal: Nat Commun / Year: 2022
Title: Watching right and wrong nucleotide insertion captures hidden polymerase fidelity checkpoints.
Authors: Jamsen, J.A. / Shock, D.D. / Wilson, S.H.
History
DepositionMar 21, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)43,86512
Polymers43,0634
Non-polymers8018
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5600 Å2
ΔGint-51 kcal/mol
Surface area17480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.750, 59.917, 141.302
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 36703.977 Da / Num. of mol.: 1 / Mutation: C543A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLL / Plasmid: pET / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9UGP5, DNA-directed DNA polymerase, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases

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DNA chain , 3 types, 3 molecules TPD

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


Mass: 3374.210 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: 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.) Homo sapiens (human)
#4: DNA chain DNA (5'-D(P*GP*CP*CP*G)-3')


Mass: 1191.818 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 5 types, 208 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-DCP / 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O13P3 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.74 Å3/Da / Density % sol: 55.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 80-95mM BICINE pH 8.3, 0.3M Na-K Tartrate, 18-22.5% PolyPure PEG

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.817→50 Å / Num. obs: 43383 / % possible obs: 99.7 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.04 / Rrim(I) all: 0.101 / Χ2: 1.103 / Net I/σ(I): 8.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.82-1.856.20.85921160.740.3670.9360.9599.8
1.85-1.896.50.81221110.7780.340.8810.96599.2
1.89-1.926.70.66621600.8280.2740.7220.98699.8
1.92-1.966.80.5521180.8870.2250.5951.03999.7
1.96-26.70.4721580.9090.1930.5091.08499.6
2-2.056.80.37621390.9470.1540.4071.111100
2.05-2.16.80.321320.9580.1230.3251.17799.7
2.1-2.166.80.25921500.9670.1060.281.2199.8
2.16-2.226.80.22521500.9760.0930.2441.26100
2.22-2.296.80.19421310.9790.080.211.27999.9
2.29-2.376.80.16321540.9830.0680.1761.19699.9
2.37-2.476.80.14221720.9890.0590.1541.24299.8
2.47-2.586.80.11921690.9880.050.1291.16299.9
2.58-2.726.80.10121560.9880.0430.111.126100
2.72-2.896.80.08921820.9920.0370.0961.0299.9
2.89-3.116.80.08421870.990.0360.0911.066100
3.11-3.436.80.07622090.9920.0320.0831.052100
3.43-3.926.80.07222120.9920.0310.0781.095100
3.92-4.946.70.07622380.9910.0330.0831.0299.6
4.94-506.30.09323390.9870.0410.1020.99498

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Processing

Software
NameVersionClassification
PHENIXv1.15.2-3472refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UPQ

3upq


Resolution: 1.817→39.212 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.254 2122 4.9 %
Rwork0.2104 41197 -
obs0.2125 43319 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 240.48 Å2 / Biso mean: 52.2665 Å2 / Biso min: 22.78 Å2
Refinement stepCycle: final / Resolution: 1.817→39.212 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2309 426 55 201 2991
Biso mean--72.21 55.09 -
Num. residues----339
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8173-1.85960.32091330.2769268098
1.8596-1.90610.29691420.26832671100
1.9061-1.95760.31231450.24712706100
1.9576-2.01520.30411400.24612705100
2.0152-2.08020.27911360.22622745100
2.0802-2.15460.25371340.22392721100
2.1546-2.24080.26681440.22382719100
2.2408-2.34280.2441490.22312716100
2.3428-2.46630.25991320.21192747100
2.4663-2.62080.26331480.21622730100
2.6208-2.82310.26541370.22182779100
2.8231-3.10710.25351510.22462742100
3.1071-3.55640.2271370.19292807100
3.5564-4.47970.23491500.18172802100
4.4797-39.2120.2621440.2158292798
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.71040.1107-0.68580.5715-0.40270.7890.0091-0.75160.50760.31230.221-0.28620.65710.68640.01510.56470.2217-0.14620.8273-0.05750.4502-8.623-27.8825.754
21.06660.5059-0.19782.14530.55461.54550.03540.07770.1144-0.02930.09910.0469-0.1447-0.01910.00010.24060.0312-0.00280.27840.00070.3309-13.323-5.8644.56
31.3493-0.3344-0.90931.17510.5032.1093-0.0198-0.38680.05430.38440.05330.07980.05630.0053-0.00010.40450.00070.02940.379-0.04910.3756-18.015-0.9922.018
40.15840.04760.05480.19180.09890.1423-0.5701-0.23250.3372-0.8380.59630.46270.6203-0.1735-0.00090.5329-0.10920.00890.48080.06450.3837-27.492-19.56726.465
50.29240.16750.22110.4201-0.42731.07090.0506-0.21820.09090.40590.53140.4503-1.0298-0.9840.02430.44150.06580.09640.50010.02860.4672-28.237-6.3139.411
60.1145-0.101-0.11180.2350.07490.24710.1453-0.40370.37420.3797-0.1088-0.2002-0.223-0.2648-0.00060.29750.0068-0.01230.3254-0.0210.287-25.75-13.5128.618
70.44840.083-0.07010.22380.17070.17060.0299-0.58520.32390.51780.09770.16291.05580.3219-0.00320.67830.05740.09290.58620.05430.4229-20.3-24.9630.697
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 252:325 )A252 - 325
2X-RAY DIFFRACTION2( CHAIN A AND RESID 326:471 )A326 - 471
3X-RAY DIFFRACTION3( CHAIN A AND RESID 472:575 )A472 - 575
4X-RAY DIFFRACTION4( CHAIN T AND RESID 1:5 )T1 - 5
5X-RAY DIFFRACTION5( CHAIN T AND RESID 6:11 )T6 - 11
6X-RAY DIFFRACTION6( CHAIN P AND RESID 1:6 )P1 - 6
7X-RAY DIFFRACTION7( CHAIN D AND RESID 1:4 )D1 - 4

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