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Basic information

Entry
Database: PDB / ID: 3fds
TitleStructural insight into recruitment of translesion DNA polymerase Dpo4 to sliding clamp PCNA
Components
  • (DNA polymerase sliding clamp ...) x 2
  • DNA polymerase IV
KeywordsTRANSFERASE / Protein-protein complex / DNA damage / DNA repair / DNA replication / DNA-binding / DNA-directed DNA polymerase / Magnesium / Metal-binding / Mutator protein / Nucleotidyltransferase
Function / homology
Function and homology information


DNA polymerase processivity factor activity / leading strand elongation / regulation of DNA replication / SOS response / error-prone translesion synthesis / mismatch repair / translesion synthesis / DNA-templated DNA replication / damaged DNA binding / DNA-directed DNA polymerase ...DNA polymerase processivity factor activity / leading strand elongation / regulation of DNA replication / SOS response / error-prone translesion synthesis / mismatch repair / translesion synthesis / DNA-templated DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / magnesium ion binding / DNA binding / cytosol
Similarity search - Function
Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / DNA polymerase type-Y, HhH motif / IMS family HHH motif / DNA polymerase IV / Proliferating cell nuclear antigen, PCNA, conserved site / Proliferating cell nuclear antigen signature 1. / Proliferating cell nuclear antigen, PCNA / Proliferating cell nuclear antigen, PCNA, N-terminal ...Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / DNA polymerase type-Y, HhH motif / IMS family HHH motif / DNA polymerase IV / Proliferating cell nuclear antigen, PCNA, conserved site / Proliferating cell nuclear antigen signature 1. / Proliferating cell nuclear antigen, PCNA / Proliferating cell nuclear antigen, PCNA, N-terminal / Proliferating cell nuclear antigen, PCNA, C-terminal / Proliferating cell nuclear antigen, N-terminal domain / Proliferating cell nuclear antigen, C-terminal domain / 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
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / DNA polymerase sliding clamp 1 / DNA polymerase IV / DNA polymerase sliding clamp 2
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
AuthorsLing, H.
CitationJournal: Mol.Microbiol. / Year: 2009
Title: Structural insight into recruitment of translesion DNA polymerase Dpo4 to sliding clamp PCNA
Authors: Xing, G. / Kirouac, K. / Shin, Y.J. / Bell, S.D. / Ling, H.
History
DepositionNov 26, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Oct 20, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 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

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Assembly

Deposited unit
A: DNA polymerase IV
C: DNA polymerase sliding clamp B
D: DNA polymerase sliding clamp C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,74836
Polymers95,2573
Non-polymers2,49133
Water5,711317
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.986, 86.414, 97.582
Angle α, β, γ (deg.)90.000, 107.300, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA polymerase IV / Pol IV


Mass: 40257.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: dbh, dpo4, SSO2448 / Plasmid: pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q97W02, DNA-directed DNA polymerase

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DNA polymerase sliding clamp ... , 2 types, 2 molecules CD

#2: Protein DNA polymerase sliding clamp B / Proliferating cell nuclear antigen homolog B / PCNA B


Mass: 27521.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: pcnB, pcnA-2, SSO0397, C41_008 / Plasmid: pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P57766
#3: Protein DNA polymerase sliding clamp C / Proliferating cell nuclear antigen homolog C / PCNA C


Mass: 27477.191 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: pcnC, pcnA-2, SSO1047 / Plasmid: pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q97Z84

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Non-polymers , 6 types, 350 molecules

#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 317 / Source method: isolated from a natural source / Formula: H2O

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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: 2.79 Å3/Da / Density % sol: 55.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10% PEG3350, 125mM LiCl, pH 7.5, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97902 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 27, 2006
RadiationMonochromator: Inserted device / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97902 Å / Relative weight: 1
ReflectionResolution: 2.05→100 Å / Num. all: 65842 / Num. obs: 64500 / % possible obs: 98.5 % / Redundancy: 3.6 % / Biso Wilson estimate: 38.7 Å2 / Rmerge(I) obs: 0.073 / Χ2: 1.434
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 3 % / Rmerge(I) obs: 0.519 / Mean I/σ(I) obs: 2 / Num. unique all: 2897 / Χ2: 0.987 / % possible all: 89.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.7 Å26.31 Å
Translation2.7 Å26.31 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 1jx4 and 2ijx

1jx4

2ijx


Resolution: 2.05→29.88 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.24 / WRfactor Rwork: 0.19 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.834 / SU B: 10.406 / SU ML: 0.143 / SU R Cruickshank DPI: 0.183 / SU Rfree: 0.169 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.183 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1300 2 %RANDOM
Rwork0.19 ---
obs0.191 63377 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 81.86 Å2 / Biso mean: 46.673 Å2 / Biso min: 15.49 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å20 Å20.81 Å2
2---0.46 Å20 Å2
3---1.53 Å2
Refinement stepCycle: LAST / Resolution: 2.05→29.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6650 0 162 317 7129
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0227083
X-RAY DIFFRACTIONr_angle_refined_deg1.8611.9979495
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.9455889
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.53824.271295
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.931151362
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0811546
X-RAY DIFFRACTIONr_chiral_restr0.1360.21088
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215095
X-RAY DIFFRACTIONr_mcbond_it0.8011.54300
X-RAY DIFFRACTIONr_mcangle_it1.45827017
X-RAY DIFFRACTIONr_scbond_it2.77832783
X-RAY DIFFRACTIONr_scangle_it4.3044.52464
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 84 -
Rwork0.253 4309 -
all-4393 -
obs--100 %
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)
17.0657-3.1879-3.00075.62083.68636.0011-0.1699-0.94430.48820.4060.0567-0.02130.2656-0.04150.1132-0.09950.09280.0031-0.0107-0.1435-0.2215-5.48229.515-11.427
26.1634-0.4-1.16586.6803-1.82386.9164-0.2435-1.1966-1.65720.94440.41062.33030.7961-1.8445-0.16720.3207-0.09150.21970.59110.27861.2151-11.009-4.039-11.761
34.6873-2.74210.22225.7256-0.50973.04340.24280.1156-0.5214-0.4178-0.11410.21520.3017-0.1362-0.1287-0.16370.0517-0.0284-0.2069-0.024-0.25554.0239.99-24.435
43.0409-0.4569-1.62076.15484.30478.6066-0.31160.0768-0.21020.37410.1453-0.11390.7479-0.24470.1663-0.1331-0.06750.0524-0.2184-0.0569-0.1047-23.57-2.946-49.465
54.4303-2.12-0.27616.78917.212320.31460.2197-0.5599-0.24840.70040.4226-0.8251.0032.6636-0.64230.00730.06940.02880.58550.00310.1118-21.359.816-18.058
62.82570.5252-1.23582.2177-2.6047.78460.0243-0.8425-0.44260.12010.15150.14140.0189-0.1872-0.1758-0.16010.00940.0210.170.2396-0.1299-43.9514.056-3.107
72.7002-0.4136-0.19892.6263-1.51035.09960.1004-0.37860.16930.353-0.04-0.1284-0.6630.5499-0.0604-0.1246-0.1030.0534-0.1168-0.002-0.2134-35.06520.899-22.217
83.61261.2150.76652.8062-0.2542.4357-0.19450.27260.2888-0.18820.13290.2879-0.12250.11590.0616-0.1341-0.02980.0334-0.22770.0997-0.0762-50.21126.096-48.543
910.65172.25141.32452.4823-0.27951.3093-0.08910.89681.1056-0.24570.05630.73260.07480.04730.0328-0.0528-0.01630.0175-0.20140.0420.0423-64.32419.962-56.058
106.59324.85250.21237.422-0.06561.5924-0.3490.72010.8444-0.56590.39121.341-0.0757-0.1094-0.0422-0.0698-0.0386-0.0728-0.12660.06320.2121-73.67815.868-55.996
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 77
2X-RAY DIFFRACTION2A173 - 239
3X-RAY DIFFRACTION3A1 - 10
4X-RAY DIFFRACTION3A78 - 172
5X-RAY DIFFRACTION4A240 - 341
6X-RAY DIFFRACTION5A342 - 351
7X-RAY DIFFRACTION6C1 - 122
8X-RAY DIFFRACTION7C123 - 249
9X-RAY DIFFRACTION8D1 - 111
10X-RAY DIFFRACTION9D112 - 146
11X-RAY DIFFRACTION10D147 - 246

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