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- PDB-4fbu: Dpo4 polymerase pre-insertion binary complex with the N-(deoxygua... -

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Basic information

Entry
Database: PDB / ID: 4fbu
TitleDpo4 polymerase pre-insertion binary complex with the N-(deoxyguanosin-8-yl)-1-aminopyrene lesion
Components
  • DNA polymerase IV
  • DNA primerPrimer (molecular biology)
  • DNA template
KeywordsTRANSFERASE/DNA / DNA polymerase / TRANSFERASE-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, Y-family, little finger domain superfamily ...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 speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsKirouac, K. / Basu, A. / Ling, H.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Structural mechanism of replication stalling on a bulky amino-polycyclic aromatic hydrocarbon DNA adduct by a y family DNA polymerase.
Authors: Kirouac, K.N. / Basu, A.K. / Ling, H.
History
DepositionMay 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2013Group: Database references
Revision 1.2Nov 13, 2013Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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
B: DNA polymerase IV
P: DNA primer
T: DNA template
D: DNA primer
C: DNA template
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,17510
Polymers95,0146
Non-polymers1604
Water4,468248
1
A: DNA polymerase IV
P: DNA primer
T: DNA template
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5875
Polymers47,5073
Non-polymers802
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-61 kcal/mol
Surface area19890 Å2
MethodPISA
2
B: DNA polymerase IV
D: DNA primer
C: DNA template
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5875
Polymers47,5073
Non-polymers802
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-59 kcal/mol
Surface area19750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.774, 181.458, 52.744
Angle α, β, γ (deg.)90.00, 109.49, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DNA polymerase IV / / Pol IV


Mass: 39019.523 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (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 primer / Primer (molecular biology)


Mass: 3880.552 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic DNA
#3: DNA chain DNA template


Mass: 4607.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic DNA
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 2.51 Å3/Da / Density % sol: 50.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2 M Ca(Ac)2, 0.1 M Hepes 7.0, 15 % PEG 3350, 2.5 % glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 30, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.6→31.24 Å / Num. all: 29148 / Num. obs: 25790 / % possible obs: 95.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.6.4_486) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→31.24 Å / SU ML: 0.38 / σ(F): 0.02 / Phase error: 28.05 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2614 1324 5.13 %
Rwork0.2175 --
obs0.2198 25790 89.95 %
all-29148 -
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.794 Å2 / ksol: 0.369 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.854 Å20 Å22.3644 Å2
2--10.0547 Å2-0 Å2
3----7.2007 Å2
Refinement stepCycle: LAST / Resolution: 2.6→31.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5467 1136 4 248 6855
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076815
X-RAY DIFFRACTIONf_angle_d1.2229391
X-RAY DIFFRACTIONf_dihedral_angle_d20.0462697
X-RAY DIFFRACTIONf_chiral_restr0.0691063
X-RAY DIFFRACTIONf_plane_restr0.004999
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.70410.31951190.32782605X-RAY DIFFRACTION86
2.7041-2.82710.37391630.30772676X-RAY DIFFRACTION89
2.8271-2.9760.37331470.29952749X-RAY DIFFRACTION91
2.976-3.16230.30441560.24612777X-RAY DIFFRACTION92
3.1623-3.40620.27061590.21912814X-RAY DIFFRACTION93
3.4062-3.74850.25131460.21662856X-RAY DIFFRACTION94
3.7485-4.28970.24591600.18482844X-RAY DIFFRACTION95
4.2897-5.40.19011500.17252748X-RAY DIFFRACTION91
5.4-31.24180.26071240.21582397X-RAY DIFFRACTION78
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)
13.1141-0.7849-1.46211.0033-0.08010.5405-0.07640.50020.4156-0.0693-0.12150.00710.12-0.18640.13460.2376-0.0507-0.05190.26480.0560.33562.4946-37.934-3.1111
22.1991-0.91981.10071.3503-0.10420.5859-0.15450.61610.450.11260.0299-0.1743-0.02820.04030.10050.2154-0.1227-0.05990.30440.08920.33523.5216-37.7758-4.844
31.79380.1060.54731.91671.17833.20030.01630.04620.74850.05610.3601-0.3315-0.48420.3233-0.32580.2794-0.10770.01360.1942-0.05720.6324-0.7053-17.03435.6721
44.0762-2.88312.30472.6105-1.03072.75870.50320.9191-0.905-0.1578-0.38170.61160.17731.078-0.07940.19520.0312-0.11270.7424-0.18890.3853-20.1982-33.5494-18.3467
52.1080.9979-1.79590.1051-1.11612.0926-0.1048-0.01810.35620.09960.03340.1776-0.22540.04890.05090.3472-0.04640.01720.1498-0.02810.2658-14.6893-55.855212.4023
61.6320.09310.02211.9164-0.69511.2997-0.39850.5539-0.2739-0.04130.2133-0.16350.3548-0.35870.21640.3676-0.11340.15670.1971-0.16760.3095-25.3165-75.395712.2412
71.5204-0.4484-0.19390.4040.07590.2274-0.1283-0.9582-0.17130.09810.4619-0.0473-0.54670.2064-0.19730.2552-0.11460.05210.4110.04920.203-26.8586-76.00524.4573
82.4261-0.25621.01641.5177-0.4560.92220.12081.0463-0.0008-0.1041-0.1876-0.1877-0.11480.36620.07420.2625-0.05920.04140.5931-0.00860.1403-7.7112-59.568839.8356
90.6687-0.778-0.191.66631.15450.95210.6598-0.1107-0.32321.4755-1.0401-0.04110.79090.35120.22641.2673-0.2582-0.05910.46130.22780.411-12.4444-76.259236.0728
102.58580.3587-1.05151.78431.42792.37280.3825-0.4060.3623-0.31180.042-0.30730.77920.8259-0.56280.55340.0301-0.00210.26590.04880.247-13.1709-76.570434.8581
112.3325-0.1751.34581.1356-0.5260.8797-0.82890.829-0.08380.44070.24830.12260.04880.69680.32340.6834-0.00670.15420.71320.03030.744-17.4426-16.8041-13.0637
120.3720.28480.20282.79370.75612.12620.33190.61680.1016-0.2123-1.38390.636-0.464-0.17640.50010.54270.2654-0.21970.8515-0.19760.7226-18.3568-17.3736-14.012
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:44)
2X-RAY DIFFRACTION2(chain A and resid 45:92)
3X-RAY DIFFRACTION3(chain A and resid 93:239)
4X-RAY DIFFRACTION4(chain A and resid 240:341)
5X-RAY DIFFRACTION5(chain B and resid 1:91)
6X-RAY DIFFRACTION6(chain B and resid 92:229)
7X-RAY DIFFRACTION7(chain B and resid 230:246)
8X-RAY DIFFRACTION8(chain B and resid 247:341)
9X-RAY DIFFRACTION9(chain C and resid 5:16)
10X-RAY DIFFRACTION10(chain D and resid 2:13)
11X-RAY DIFFRACTION11(chain P and resid 2:13)
12X-RAY DIFFRACTION12(chain T and resid 5:16)

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