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- PDB-6l97: Complex of DNA polymerase IV and L-DNA duplex -

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Basic information

Entry
Database: PDB / ID: 6l97
TitleComplex of DNA polymerase IV and L-DNA duplex
Components
  • DNA (5'-D(*(0DG)P*(0DG)P*(0DG)P*(0DG)P*(0DG)P*(0DA)P*(0DA)P*(0DG)P*(0DG)P*(0DA)P*(0DT)P*(0DT)P*(0DC)P*(0DC))-3')
  • DNA (5'-D(P*(0DG)P*(0DG)P*(0DA)P*(0DA)P*(0DT)P*(0DC)P*(0DC)P*(0DT)P*(0DT)P*(0DC)P*(0DC)P*(0DC)P*(0DC)P*(0DC))-3')
  • DNA polymerase IV
KeywordsDNA BINDING PROTEIN/DNA / Dpo4 / L-DNA duplex / DNA polymerase / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


error-prone translesion synthesis / DNA-templated DNA replication / DNA-directed DNA polymerase / damaged DNA binding / DNA-directed DNA polymerase activity / magnesium ion binding / cytoplasm
Similarity search - Function
DNA polymerase type-Y, HhH motif / IMS family HHH motif / DNA polymerase IV / : / DNA polymerase, Y-family, little finger domain / MutS, DNA mismatch repair protein, domain I - #60 / MutS, DNA mismatch repair protein, domain I / DNA polymerase, Y-family, little finger domain / impB/mucB/samB family C-terminal domain / UmuC domain ...DNA polymerase type-Y, HhH motif / IMS family HHH motif / DNA polymerase IV / : / DNA polymerase, Y-family, little finger domain / MutS, DNA mismatch repair protein, domain I - #60 / MutS, DNA mismatch repair protein, domain I / DNA polymerase, Y-family, little finger domain / impB/mucB/samB family C-terminal domain / UmuC domain / DNA polymerase, Y-family, little finger domain superfamily / impB/mucB/samB family / UmuC domain profile. / Reverse transcriptase/Diguanylate cyclase domain / Dna Ligase; domain 1 / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA polymerase IV
Similarity search - Component
Biological speciesSaccharolobus solfataricus (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.362 Å
AuthorsChung, H.S. / An, J. / Hwang, D.
CitationJournal: Chem.Commun.(Camb.) / Year: 2020
Title: The crystal structure of a natural DNA polymerase complexed with mirror DNA.
Authors: An, J. / Choi, J. / Hwang, D. / Park, J. / Pemble 4th, C.W. / Duong, T.H.M. / Kim, K.R. / Ahn, H. / Chung, H.S. / Ahn, D.R.
History
DepositionNov 8, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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 IV
B: DNA polymerase IV
T: DNA (5'-D(P*(0DG)P*(0DG)P*(0DA)P*(0DA)P*(0DT)P*(0DC)P*(0DC)P*(0DT)P*(0DT)P*(0DC)P*(0DC)P*(0DC)P*(0DC)P*(0DC))-3')
P: DNA (5'-D(*(0DG)P*(0DG)P*(0DG)P*(0DG)P*(0DG)P*(0DA)P*(0DA)P*(0DG)P*(0DG)P*(0DA)P*(0DT)P*(0DT)P*(0DC)P*(0DC))-3')


Theoretical massNumber of molelcules
Total (without water)92,4164
Polymers92,4164
Non-polymers00
Water2,072115
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.861, 54.969, 96.545
Angle α, β, γ (deg.)90.000, 113.390, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DNA polymerase IV / Pol IV


Mass: 41329.020 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (archaea)
Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: dbh, dpo4, SSO2448 / Production host: Escherichia coli (E. coli) / References: UniProt: Q97W02, DNA-directed DNA polymerase
#2: DNA chain DNA (5'-D(P*(0DG)P*(0DG)P*(0DA)P*(0DA)P*(0DT)P*(0DC)P*(0DC)P*(0DT)P*(0DT)P*(0DC)P*(0DC)P*(0DC)P*(0DC)P*(0DC))-3')


Mass: 5372.480 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*(0DG)P*(0DG)P*(0DG)P*(0DG)P*(0DG)P*(0DA)P*(0DA)P*(0DG)P*(0DG)P*(0DA)P*(0DT)P*(0DT)P*(0DC)P*(0DC))-3')


Mass: 4385.852 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.26 Å3/Da / Density % sol: 45.64 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Sodium formate, 0.05 M BICINE (pH 8.5), 10% w/v Polyethylene glycol monomethyl ether 5,000, and 1.1% benzamidine-HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.36→50 Å / Num. obs: 33537 / % possible obs: 97.9 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.062 / Rrim(I) all: 0.14 / Χ2: 3.332 / Net I/σ(I): 18.4 / Num. measured all: 153932
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.36-2.4430.55532380.1640.3420.6561.5695.3
2.44-2.543.40.52732910.2930.3090.6151.74896.7
2.54-2.663.80.4633030.4370.2610.5311.88997.8
2.66-2.84.20.36533300.7350.1960.4162.11898.4
2.8-2.974.50.27233830.8740.1380.3062.45498.9
2.97-3.250.18433980.9820.0890.2052.99499.5
3.2-3.535.50.14934020.9860.0680.1653.39499.6
3.53-4.035.80.12334180.9820.0550.1354.05399.7
4.03-5.085.50.09434220.9880.0440.1054.80198.6
5.08-5050.0833520.9890.0410.095.53694.6

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Processing

Software
NameVersionClassification
PHENIX1.15_3459refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2bq3

2bq3


Resolution: 2.362→34.496 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 28.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2658 2013 6.01 %
Rwork0.2298 31479 -
obs0.232 33492 97.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 144.47 Å2 / Biso mean: 66.782 Å2 / Biso min: 21.48 Å2
Refinement stepCycle: final / Resolution: 2.362→34.496 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5402 572 22 115 6111
Biso mean--72.69 57.86 -
Num. residues----699
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.362-2.4210.31031240.3046209992
2.421-2.48640.38541460.2916219596
2.4864-2.55960.2751470.2807219297
2.5596-2.64220.32771430.2906224598
2.6422-2.73660.29431370.2849226598
2.7366-2.84610.2811550.2728223599
2.8461-2.97550.32311460.2667225799
2.9755-3.13230.30691380.2596228299
3.1323-3.32840.26981440.2418228199
3.3284-3.58520.29971450.23072311100
3.5852-3.94550.26131450.21242311100
3.9455-4.51530.22521470.1912226699
4.5153-5.68470.25361480.2042230599
5.6847-34.4960.23041480.2164223593
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)
1-0.20340.72420.36560.6309-0.8160.9071-0.34270.04910.0326-0.48750.57380.09710.3279-0.08440.10290.6754-0.03310.00220.31430.06460.3793-57.9184-39.19159.0312
21.3819-0.0216-0.75181.19050.07081.6956-0.182-0.29690.32190.08870.1604-0.2787-0.15780.24450.00020.4340.0701-0.01020.3697-0.0660.2888-53.3831-18.77129.8393
31.80850.11880.63520.0138-0.13160.61-0.0670.1006-0.17040.01910.08180.0609-0.2051-0.12660.0030.44880.08810.05740.3402-0.07130.3315-64.7863-19.635225.4124
43.1210.48450.01822.9277-1.02922.1925-0.16890.0677-0.28120.0258-0.1415-0.4793-0.03420.287-0.8120.2331-0.01070.09170.26620.02380.2632-30.3843-23.774942.0844
50.6473-0.3753-0.14930.2330.33680.2454-0.1699-0.1236-0.1273-0.16090.00830.0635-0.15420.0423-0.00780.5644-0.2004-0.13910.50130.1870.516-25.3266-42.110378.7838
6-0.0241-0.291-0.17562.96490.25040.0471-0.1086-0.2910.20791.386-0.2467-0.96190.59320.09060.03590.6423-0.0782-0.05130.82790.27841.1233-17.1713-50.633772.8074
70.17-0.0178-0.06710.12230.17030.276-0.12671.3149-0.78590.0381-0.1171-0.14990.08410.3229-0.02310.7121-0.11190.08590.8170.20051.1431-15.5905-54.515771.9482
80.8131-0.0416-0.61821.04840.74081.04480.1625-0.3074-0.03040.2976-0.0995-0.114-0.048-0.2504-0.00270.3834-0.1361-0.0720.37610.12260.2539-19.4265-27.255676.4675
90.5382-0.37730.85470.645-0.59340.5246-0.41330.06030.1584-0.0897-0.09150.0872-0.5862-0.2519-0.38960.4396-0.1765-0.00430.18980.150.194-23.6481-23.779156.9458
102.15981.33680.87584.6420.01341.732-0.12820.35330.1448-0.25950.15360.8758-0.2867-0.5278-0.01310.283-0.06560.02870.26760.05140.4328-51.2595-25.693446.5146
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 77 )A1 - 77
2X-RAY DIFFRACTION2chain 'A' and (resid 78 through 177 )A78 - 177
3X-RAY DIFFRACTION3chain 'A' and (resid 178 through 257 )A178 - 257
4X-RAY DIFFRACTION4chain 'A' and (resid 258 through 341 )A258 - 341
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 27 )B1 - 27
6X-RAY DIFFRACTION6chain 'B' and (resid 28 through 53 )B28 - 53
7X-RAY DIFFRACTION7chain 'B' and (resid 54 through 77 )B54 - 77
8X-RAY DIFFRACTION8chain 'B' and (resid 78 through 209 )B78 - 209
9X-RAY DIFFRACTION9chain 'B' and (resid 210 through 257 )B210 - 257
10X-RAY DIFFRACTION10chain 'B' and (resid 258 through 341 )B258 - 341

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