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- PDB-6l84: Complex of DNA polymerase IV and D-DNA duplex -

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Basic information

Entry
Database: PDB / ID: 6l84
TitleComplex of DNA polymerase IV and D-DNA duplex
Components
  • DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*CP*C)-3')
  • DNA (5'-D(P*CP*GP*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3')
  • DNA polymerase IV
KeywordsDNA BINDING PROTEIN/DNA / Dpo4 / D-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 / damaged DNA binding / DNA-directed DNA polymerase / 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 / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / DNA/RNA polymerase superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / 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: 2.602 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 4, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)51,2086
Polymers51,0873
Non-polymers1203
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-80 kcal/mol
Surface area20230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.763, 98.664, 100.769
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein DNA polymerase IV / Pol IV


Mass: 41329.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: SF file contains Friedel pairs.
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(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*CP*C)-3')


Mass: 4385.852 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SF file contains Friedel pairs. / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*CP*GP*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3')


Mass: 5372.480 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SF file contains Friedel pairs. / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.57 Å3/Da / Density % sol: 56.02 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 0.1 M BIS-TRIS (pH 7.0), 0.1 M calcium acetate, 2% glycerol, and 9% w/v PEG3350

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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: Jul 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 26904 / % possible obs: 99.8 % / Redundancy: 11.3 % / Biso Wilson estimate: 33.76 Å2 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.036 / Rrim(I) all: 0.127 / Χ2: 0.951 / Net I/σ(I): 11.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.647.70.3598350.8580.1330.3840.99399.8
2.64-2.698.60.3417910.9040.1180.3620.93199.9
2.69-2.748.70.3238280.9110.1120.3420.9399.8
2.74-2.89.20.288190.9560.0930.2960.96899.6
2.8-2.869.50.278140.9540.0890.2850.94399.9
2.86-2.939.70.238270.9730.0740.2420.91699.9
2.93-310.20.1998080.9790.0630.2090.93699.9
3-3.0810.30.1898320.9840.0590.1980.95899.8
3.08-3.1710.90.1638080.9880.0490.170.94399.8
3.17-3.2811.60.1388350.9920.040.1440.928100
3.28-3.3911.90.1248250.9930.0360.1290.92799.6
3.39-3.5312.30.1148310.9940.0330.1190.86899.9
3.53-3.6912.70.1128160.9930.0310.1170.88199.9
3.69-3.8812.90.1058340.9940.0290.1090.851100
3.88-4.1313.20.1028400.9930.0280.1060.838100
4.13-4.4513.60.18440.9950.0270.1040.855100
4.45-4.8913.60.118500.9950.030.1140.992100
4.89-5.613.40.1288510.9940.0350.1331.25299.9
5.6-7.0513.20.1138750.9930.0320.1181.019100
7.05-5012.40.1189320.9810.0360.1231.04299

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2bq3

2bq3


Resolution: 2.602→44.872 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.53 / Phase error: 21.92
RfactorNum. reflection% reflection
Rfree0.2263 2723 10.12 %
Rwork0.1824 --
obs0.1869 26904 86.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 127.72 Å2 / Biso mean: 42.7304 Å2 / Biso min: 10.59 Å2
Refinement stepCycle: final / Resolution: 2.602→44.872 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2743 590 3 108 3444
Biso mean--52.76 40.81 -
Num. residues----370
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6025-2.64980.3486800.268270847
2.6498-2.70070.2862860.259981456
2.7007-2.75580.27191030.260888360
2.7558-2.81580.31551080.22898067
2.8158-2.88130.2561180.2265106972
2.8813-2.95330.24871370.2266115479
2.9533-3.03310.27531410.2263124785
3.0331-3.12240.24541490.2231132789
3.1224-3.22310.27221420.2106137495
3.2231-3.33830.22361540.1913145297
3.3383-3.47190.27681580.1765145198
3.4719-3.62980.22051650.1696144499
3.6298-3.82110.21871740.16971476100
3.8211-4.06040.21061680.15971484100
4.0604-4.37360.18891700.13671456100
4.3736-4.81330.16741640.14181478100
4.8133-5.50870.21871660.15521460100
5.5087-6.93630.19721710.20141471100
6.9363-44.8720.2271690.1834145398
Refinement TLS params.Method: refined / Origin x: -16.5985 Å / Origin y: -21.7208 Å / Origin z: 17.6586 Å
111213212223313233
T0.0876 Å2-0.0482 Å2-0.0144 Å2-0.1247 Å2-0.0296 Å2--0.107 Å2
L0.4128 °2-0.2048 °2-0.2508 °2-0.9925 °2-0.062 °2--0.706 °2
S-0.0164 Å °-0.1105 Å °0.0608 Å °0.0585 Å °0.0846 Å °-0.1184 Å °0.0783 Å °0.0627 Å °0.0198 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 341
2X-RAY DIFFRACTION1allP1 - 14
3X-RAY DIFFRACTION1allT1 - 15
4X-RAY DIFFRACTION1allB1 - 3
5X-RAY DIFFRACTION1allS1 - 108

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