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- PDB-2xc9: BINARY COMPLEX OF SULFOLOBUS SOLFATARICUS DPO4 DNA POLYMERASE AND... -

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Basic information

Entry
Database: PDB / ID: 2xc9
TitleBINARY COMPLEX OF SULFOLOBUS SOLFATARICUS DPO4 DNA POLYMERASE AND 1, N2-ETHENOGUANINE MODIFIED DNA, MAGNESIUM FORM
Components
  • 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*CP*G)-3'
  • 5'-D(*TP*CP*AP*CP*GNEP*GP*AP*AP*TP*CP*CP*TP*TP* CP*CP*CP*CP*C)-3'
  • DNA POLYMERASE IV
KeywordsTRANSFERASE/DNA / TRANSFERASE-DNA COMPLEX / TRANSLESION NUCLEOTIDYLTRANSFERASE
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 speciesSULFOLOBUS SOLFATARICUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsIrimia, A. / Loukachevitch, L.V. / Egli, M.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Metal Ion Dependence of the Active Site Conformation of the Trans-Lesion DNA Polymerase Dpo4 from Sulfolobus Solfataricus
Authors: Irimia, A. / Loukachevitch, L.V. / Eoff, R.L. / Guengerich, F.P. / Egli, M.
History
DepositionApr 20, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2012Group: Database references / Refinement description / Version format compliance
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA POLYMERASE IV
P: 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*CP*G)-3'
T: 5'-D(*TP*CP*AP*CP*GNEP*GP*AP*AP*TP*CP*CP*TP*TP* CP*CP*CP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)50,9093
Polymers50,9093
Non-polymers00
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint-38.6 kcal/mol
Surface area20230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.722, 102.125, 53.004
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein DNA POLYMERASE IV / POL IV


Mass: 41086.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Strain: P2 / Gene: DPO4 / Plasmid: PET22B/DPO4-NHIS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q97W02, DNA-directed DNA polymerase
#2: DNA chain 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*CP*G)-3' / 14-MER PRIMER


Mass: 4425.876 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain 5'-D(*TP*CP*AP*CP*GNEP*GP*AP*AP*TP*CP*CP*TP*TP* CP*CP*CP*CP*C)-3' / 18-MER TEMPLATE


Mass: 5396.503 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE N-TERMINAL 6 RESIDUES HIS TAG ARE DISORDERED AND MISSING FROM THE STRUCTURE. THE C-TERMINAL 11 ...THE N-TERMINAL 6 RESIDUES HIS TAG ARE DISORDERED AND MISSING FROM THE STRUCTURE. THE C-TERMINAL 11 RESIDUES ARE DISORDERED AND ABSENT FROM THE STRUCTURE.

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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: 3.16 Å3/Da / Density % sol: 48.08 %
Description: THE MODEL POSITION WAS OPTIMIZED BY SEVERAL ROUNDS OF RIGID BODY REFINEMENT.
Crystal growpH: 7.5
Details: 12-20% POLYETHYLENE GLYCOL 3350, 0.2 M AMMONIUM ACETATE, 0.1 M MAGNESIUM ACETATE, AND 20 MM TRIS (PH 7.5)

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 12, 2006
Details: ROSENBAUM-ROCK MONOCHROMATOR HIGH -RESOLUTION DOUBLE-CRYSTAL SI (111) SAGITTAL FOCUSING. ROSENBAUM-ROCK VERTICAL FOCUSING MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→26.91 Å / Num. obs: 26245 / % possible obs: 99.3 % / Observed criterion σ(I): 1 / Redundancy: 12.6 % / Biso Wilson estimate: 43.4 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 36.3
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 6.2 / % possible all: 99.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BQ3

2bq3


Resolution: 2.2→26.91 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1362679.09 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1270 4.8 %RANDOM
Rwork0.221 ---
obs0.221 26245 99.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.325 Å2 / ksol: 0.309453 e/Å3
Displacement parametersBiso mean: 40.7 Å2
Baniso -1Baniso -2Baniso -3
1-6.44 Å20 Å20 Å2
2---2.43 Å20 Å2
3----4.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.29 Å
Luzzati d res low-50 Å
Luzzati sigma a0.3 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.2→26.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2744 617 0 247 3608
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.08
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.421.5
X-RAY DIFFRACTIONc_mcangle_it2.322
X-RAY DIFFRACTIONc_scbond_it2.072
X-RAY DIFFRACTIONc_scangle_it3.192.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.303 226 5.3 %
Rwork0.277 4015 -
obs--98.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_NEW.PARAMDNA-RNA_NEW.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP

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