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- PDB-6ueu: Crystal structure of BF DNA polymerase F710Y mutant bound to tetr... -

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Basic information

Entry
Database: PDB / ID: 6ueu
TitleCrystal structure of BF DNA polymerase F710Y mutant bound to tetrahydrofuran and dATP
Components
  • DNA (5'-D(*CP*GP*(3DR)P*AP*CP*GP*TP*GP*AP*TP*CP*G)-3')
  • DNA (5'-D(*CP*GP*AP*TP*CP*AP*CP*GP*(2DT))-3')
  • DNA polymerase I
KeywordsREPLICATION
Function / homology
Function and homology information


3'-5' exonuclease activity / DNA-templated DNA replication / double-strand break repair / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding / metal ion binding
Similarity search - Function
: / DNA polymerase I, ribonuclease H-like domain / DNA polymerase 1 / Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / 3'-5' exonuclease / 3'-5' exonuclease domain / DNA polymerase A / DNA polymerase family A / DNA-directed DNA polymerase, family A, conserved site ...: / DNA polymerase I, ribonuclease H-like domain / DNA polymerase 1 / Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / 3'-5' exonuclease / 3'-5' exonuclease domain / DNA polymerase A / DNA polymerase family A / DNA-directed DNA polymerase, family A, conserved site / DNA polymerase family A signature. / DNA-directed DNA polymerase, family A, palm domain / DNA polymerase A domain / 5' to 3' exonuclease, C-terminal subdomain / Ribonuclease H-like superfamily/Ribonuclease H / DNA polymerase; domain 1 / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
sucrose / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase I
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWu, E.Y. / Beese, L.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RO1 GM091487 United States
CitationJournal: To Be Published
Title: Structural basis for blockage of DNA synthesis by a thymine dimer lesion in a high-fidelity DNA polymerase
Authors: Walsh, A.R. / Beese, L.S. / Wu, E.Y.
History
DepositionSep 23, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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
A: DNA polymerase I
D: DNA polymerase I
B: DNA (5'-D(*CP*GP*AP*TP*CP*AP*CP*GP*(2DT))-3')
C: DNA (5'-D(*CP*GP*(3DR)P*AP*CP*GP*TP*GP*AP*TP*CP*G)-3')
E: DNA (5'-D(*CP*GP*AP*TP*CP*AP*CP*GP*(2DT))-3')
F: DNA (5'-D(*CP*GP*(3DR)P*AP*CP*GP*TP*GP*AP*TP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,67912
Polymers144,7986
Non-polymers1,8816
Water15,583865
1
A: DNA polymerase I
B: DNA (5'-D(*CP*GP*AP*TP*CP*AP*CP*GP*(2DT))-3')
C: DNA (5'-D(*CP*GP*(3DR)P*AP*CP*GP*TP*GP*AP*TP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,2325
Polymers72,3993
Non-polymers8332
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7250 Å2
ΔGint-19 kcal/mol
Surface area27680 Å2
MethodPISA
2
D: DNA polymerase I
E: DNA (5'-D(*CP*GP*AP*TP*CP*AP*CP*GP*(2DT))-3')
F: DNA (5'-D(*CP*GP*(3DR)P*AP*CP*GP*TP*GP*AP*TP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4477
Polymers72,3993
Non-polymers1,0484
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7090 Å2
ΔGint-19 kcal/mol
Surface area27270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.875, 109.068, 150.096
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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DNA chain , 2 types, 4 molecules BECF

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


Mass: 2699.800 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*CP*GP*(3DR)P*AP*CP*GP*TP*GP*AP*TP*CP*G)-3')


Mass: 3554.306 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Protein / Sugars , 2 types, 4 molecules AD

#1: Protein DNA polymerase I


Mass: 66144.836 Da / Num. of mol.: 2 / Mutation: F710Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: DPO1, polA
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: D9N168, DNA-directed DNA polymerase
#4: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 869 molecules

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


Mass: 491.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 865 / 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: 2.65 Å3/Da / Density % sol: 53.64 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 50% (v/v) saturated ammonium sulfate, 20 mM MgSO4, 100 mM MES, 1% MPD

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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: Jul 6, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→44.987 Å / Num. obs: 138448 / % possible obs: 96.9 % / Redundancy: 4.572 % / Biso Wilson estimate: 21.36 Å2 / Rmerge F obs: 0.132 / Rmerge(I) obs: 0.078 / Rrim(I) all: 0.089 / Net I/σ(I): 12.27 / Num. measured all: 632948
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.8-1.94.4680.6140.5952.799419121153210820.67899.7
1.9-2.194.5050.3120.2945.4118757041816416320.33599.6
2.19-2.44.5540.1560.1599.448502818955186700.1898.5
2.4-2.684.5950.1040.10713.047578916960164950.12197.3
2.68-3.14.6520.0650.07417.556764615331145400.08494.8
3.1-3.794.6760.0360.0524.845527912797118220.05792.4
3.79-5.344.7250.0260.04132.04430751002391160.04591
5.34-44.9874.7870.0220.03735.8824370583150910.04187.3

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.25data extraction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HVI

2hvi


Resolution: 1.8→44.987 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.68
RfactorNum. reflection% reflection
Rfree0.2423 6922 5 %
Rwork0.2003 --
obs0.2024 138444 96.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 102.12 Å2 / Biso mean: 33.31 Å2 / Biso min: 7.85 Å2
Refinement stepCycle: final / Resolution: 1.8→44.987 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9304 828 119 865 11116
Biso mean--36.23 34.32 -
Num. residues----1202
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8-1.82050.32522340.2898445299
1.8205-1.84190.3242350.28274463100
1.8419-1.86430.29112340.27034435100
1.8643-1.88790.3072360.26884495100
1.8879-1.91280.30372370.26414490100
1.9128-1.9390.31422340.25134446100
1.939-1.96670.28412350.24024474100
1.9667-1.9960.26682360.23324477100
1.996-2.02720.26692350.22434464100
2.0272-2.06050.26452350.2156447499
2.0605-2.0960.26762350.2164445999
2.096-2.13410.25262350.20834475100
2.1341-2.17520.25972350.2056445099
2.1752-2.21960.24442330.203443999
2.2196-2.26780.25972330.2013443099
2.2678-2.32060.23242340.1902443899
2.3206-2.37860.23332330.1916443298
2.3786-2.44290.24562320.1939440198
2.4429-2.51480.24052310.1909438997
2.5148-2.59590.23842320.1887441397
2.5959-2.68870.25092290.191435497
2.6887-2.79640.24822290.195434896
2.7964-2.92360.24232270.1914430395
2.9236-3.07770.23072230.1973423594
3.0777-3.27050.24982240.1888425393
3.2705-3.52290.20932210.1786420992
3.5229-3.87720.20952220.173421092
3.8772-4.43790.22352210.1766420191
4.4379-5.58960.20652210.1824419590
5.5896-44.9870.24232210.2162421887

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