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- PDB-2c28: Efficient and High Fidelity Incorporation of dCTP Opposite 7,8- D... -

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Basic information

Entry
Database: PDB / ID: 2c28
TitleEfficient and High Fidelity Incorporation of dCTP Opposite 7,8- Dihydro-8-oxodeoxyguanosine by Sulfolobus solfataricus DNA Polymerase Dpo4
Components
  • 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *TP*TP*C)-3'
  • 5'-D(TP*CP*AP*C 8OGP*GP*AP*AP*TP*CP*CP*TP *TP*CP*CP*CP*CP*C)-3'
  • DNA POLYMERASE IV
KeywordsPOLYMERASE / 7 / 8-DIHYDRO-8-OXODEOXYGUANOSINE / P2 DNA POLYMERASE IV / TRANSLESION DNA POLYMERASE / DDGTP / NUCLEOTIDYLTRANSFERASE / TRANSFERASE / DNA DAMAGE / DNA REPAIR / DNA REPLICATION / DNA- BINDING / DNA-DIRECTED DNA POLYMERASE / MAGNESIUM / METAL- BINDING / MUTATOR PROTEIN
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
2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE / DNA / DNA (> 10) / DNA polymerase IV
Similarity search - Component
Biological speciesSULFOLOBUS SOLFATARICUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsIrimia, A. / Loukachevitch, L.V. / Egli, M.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Efficient and High Fidelity Incorporation of Dctp Opposite 7,8-Dihydro-8-Oxodeoxyguanosine by Sulfolobus Solfataricus DNA Polymerase Dpo4
Authors: Zang, H. / Irimia, A. / Choi, J.-Y. / Angel, K.C. / Loukachevitch, L.V. / Egli, M. / P Guengerich, F.
History
DepositionSep 26, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2005Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 2, 2022Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type
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_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_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
Revision 1.4Jan 31, 2024Group: 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

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*C)-3'
T: 5'-D(TP*CP*AP*C 8OGP*GP*AP*AP*TP*CP*CP*TP *TP*CP*CP*CP*CP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0397
Polymers50,5723
Non-polymers4674
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)93.355, 102.030, 52.826
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 1 molecules A

#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 / Description: GENE DPO4 / 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, 2 molecules PT

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


Mass: 4096.670 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 13-MER PRIMER
#3: DNA chain 5'-D(TP*CP*AP*C 8OGP*GP*AP*AP*TP*CP*CP*TP *TP*CP*CP*CP*CP*C)-3'


Mass: 5388.480 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: 18-MER TEMPLATE CONTAINING A 7,8-DIHYDRO-8-OXODEOXYGUANOSINE

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Non-polymers , 3 types, 102 molecules

#4: Chemical ChemComp-DG / 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE / Deoxyguanosine monophosphate


Type: DNA linking / Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: dGMP*YM
#5: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsINVOLVEMENT IN UNTARGETED MUTAGENESIS.

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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: 2.6 Å3/Da / Density % sol: 50.96 %
Description: THE STARTING MODEL WAS THE PDB FILE WITH THE ACCESSION CODE 2BR0. ITS POSITION WAS OPTIMIZED BY SEVERAL ROUNDS OF RIGID BODY REFINEMENT
Crystal growpH: 7.5
Details: 5% PEG 3350,0.010 M TRIS-HCL PH 7.5, 100 MM CA(CH3CO2)2, 1.25% GLYCEROL, 30 MM NACL

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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: Aug 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.27→31.96 Å / Num. obs: 23827 / % possible obs: 99.7 % / Observed criterion σ(I): 1 / Redundancy: 7.08 % / Biso Wilson estimate: 56.2 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.41
Reflection shellResolution: 2.27→2.42 Å / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
X-GENdata reduction
X-GENdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BR0

2br0


Resolution: 2.27→31.96 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1204106.46 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1159 4.9 %RANDOM
Rwork0.239 ---
obs0.239 23819 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.7616 Å2 / ksol: 0.331059 e/Å3
Displacement parametersBiso mean: 53.8 Å2
Baniso -1Baniso -2Baniso -3
1-5.1 Å20 Å20 Å2
2---8.28 Å20 Å2
3---3.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.35 Å
Luzzati d res low-31.96 Å
Luzzati sigma a0.41 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.27→31.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2744 609 21 98 3472
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.11
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.51.5
X-RAY DIFFRACTIONc_mcangle_it2.462
X-RAY DIFFRACTIONc_scbond_it2.212
X-RAY DIFFRACTIONc_scangle_it3.552.5
LS refinement shellResolution: 2.27→2.42 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.356 192 4.9 %
Rwork0.341 3719 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA1.PARAMDNA-RNA1.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION4DDGTP.PARAMDDGTP.TOP
X-RAY DIFFRACTION5ION.PARAMION.TOP

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