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- PDB-2va2: Complex structure of Sulfolobus solfataricus DPO4 and DNA duplex ... -

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Basic information

Entry
Database: PDB / ID: 2va2
TitleComplex structure of Sulfolobus solfataricus DPO4 and DNA duplex containing a hydrophobic thymine isostere 2,4-difluorotoluene nucleotide in the template strand
Components
  • 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *CP*TP*A)-3'
  • 5'-D(*TP*TP*CP*AP*GP*DFTP*AP*GP*TP*CP*CP *TP*TP*CP*CP*CP*CP*C)-3'
  • DNA POLYMERASE IV
KeywordsTRANSFERASE/DNA / TRANSFERASE-DNA COMPLEX / DNA-DIRECTED DNA POLYMERASE / P2 DNA POLYMERASE IV / TRANSFERASE / NUCLEOTIDYLTRANSFERASE / MUTATOR PROTEIN / DNA REPLICATION / DNA REPAIR / DNA-BINDING / METAL-BINDING / TRANSLESION DNA POLYMERASE / 2 / DDCTP / MAGNESIUM / DNA DAMAGE
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 / 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
2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase IV
Similarity search - Component
Biological speciesSULFOLOBUS SOLFATARICUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsIrimia, A. / Pallan, P.S. / Egli, M.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Structure and Activity of Y-Class DNA Polymerase Dpo4 from Sulfolobus Solfataricus with Templates Containing the Hydrophobic Thymine Analog 2,4- Difluorotoluene.
Authors: Irimia, A. / Eoff, R.L. / Pallan, P.S. / Guengerich, F.P. / Egli, M.
History
DepositionAug 28, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2014Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Dec 13, 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
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 / _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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.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
C: 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *CP*TP*A)-3'
D: 5'-D(*TP*TP*CP*AP*GP*DFTP*AP*GP*TP*CP*CP *TP*TP*CP*CP*CP*CP*C)-3'
E: 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *CP*TP*A)-3'
F: 5'-D(*TP*TP*CP*AP*GP*DFTP*AP*GP*TP*CP*CP *TP*TP*CP*CP*CP*CP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,28914
Polymers101,1466
Non-polymers1,1438
Water3,909217
1
A: DNA POLYMERASE IV
C: 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *CP*TP*A)-3'
D: 5'-D(*TP*TP*CP*AP*GP*DFTP*AP*GP*TP*CP*CP *TP*TP*CP*CP*CP*CP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1447
Polymers50,5733
Non-polymers5714
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6090 Å2
ΔGint-56.9 kcal/mol
Surface area19780 Å2
MethodPISA
2
B: DNA POLYMERASE IV
E: 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *CP*TP*A)-3'
F: 5'-D(*TP*TP*CP*AP*GP*DFTP*AP*GP*TP*CP*CP *TP*TP*CP*CP*CP*CP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1447
Polymers50,5733
Non-polymers5714
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6460 Å2
ΔGint-61.1 kcal/mol
Surface area19920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.139, 101.875, 111.062
Angle α, β, γ (deg.)90.00, 94.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein DNA POLYMERASE IV / POL IV


Mass: 41086.754 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: DPO4 / Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Strain: P2 / Plasmid: PET22B-DPO4-NHIS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q97W02, DNA-directed DNA polymerase

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DNA chain , 2 types, 4 molecules CEDF

#2: DNA chain 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *CP*TP*A)-3'


Mass: 4105.685 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: 13-MER PRIMER
#3: DNA chain 5'-D(*TP*TP*CP*AP*GP*DFTP*AP*GP*TP*CP*CP *TP*TP*CP*CP*CP*CP*C)-3'


Mass: 5380.484 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: 18-MER TEMPLATE

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Non-polymers , 3 types, 225 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-DCT / 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE


Type: DNA linking / Mass: 451.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16N3O12P3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 2.99 Å3/Da / Density % sol: 58.9 % / Description: NONE
Crystal growpH: 7.4
Details: 30 MM NACL, 2%GLYCEROL, 10 MM TRIS PH 7.5, 2.5 MM CACL2, 0.5 MM DDCTP, 6% PEG 3350,0.1 MM AMMONIUM ACETATE, 0.05 CALCIUM ACETATE

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 17, 2007 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→22.57 Å / Num. obs: 27671 / % possible obs: 99.7 % / Observed criterion σ(I): 1 / Redundancy: 4.1 % / Biso Wilson estimate: 41.1 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.3
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.42 / % possible all: 99.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BQ3

2bq3


Resolution: 2.8→22.57 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 950150.29 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1383 4.9 %RANDOM
Rwork0.211 ---
obs0.211 28485 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.9003 Å2 / ksol: 0.326837 e/Å3
Displacement parametersBiso mean: 51.4 Å2
Baniso -1Baniso -2Baniso -3
1--12.07 Å20 Å20.29 Å2
2--15.95 Å20 Å2
3----3.87 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.59 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 2.8→22.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5516 1222 60 217 7015
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_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.96
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.31.5
X-RAY DIFFRACTIONc_mcangle_it2.272
X-RAY DIFFRACTIONc_scbond_it1.752
X-RAY DIFFRACTIONc_scangle_it2.832.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.38 233 4.9 %
Rwork0.338 4491 -
obs--99.8 %
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
X-RAY DIFFRACTION4DDCTP.PARAMDDCTP.TOP
X-RAY DIFFRACTION5ION.PARAMION.TOP

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