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- PDB-3v6j: Replication of N2,3-Ethenoguanine by DNA Polymerases -

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Basic information

Entry
Database: PDB / ID: 3v6j
TitleReplication of N2,3-Ethenoguanine by DNA Polymerases
Components
  • DNA (5'-D(*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*(DOC))-3')
  • DNA (5'-D(*TP*CP*AP*TP*(EFG)P*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*C)-3')
  • DNA polymerase IV
KeywordsTRANSFERASE/DNA / Sulfolobus solfataricus DNA polymerase IV / Dpo4 / ethenoguanine / DNA adduct / DNA lesion / DNA polymerase / DNA replication / lesion bypass / 2'-fluoro arabinose / N2 / 3-ethenoguanine / 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
2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase IV
Similarity search - Component
Biological speciesSulfolobus solfataricus P2 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsZhao, L.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2012
Title: Replication of n(2) ,3-ethenoguanine by DNA polymerases.
Authors: Zhao, L. / Christov, P.P. / Kozekov, I.D. / Pence, M.G. / Pallan, P.S. / Rizzo, C.J. / Egli, M. / Guengerich, F.P.
History
DepositionDec 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq / 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 / _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.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_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details / _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
J: DNA polymerase IV
P: DNA (5'-D(*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*(DOC))-3')
B: DNA (5'-D(*TP*CP*AP*TP*(EFG)P*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*C)-3')
K: DNA (5'-D(*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*(DOC))-3')
M: DNA (5'-D(*TP*CP*AP*TP*(EFG)P*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,79413
Polymers97,7396
Non-polymers1,0567
Water2,918162
1
A: DNA polymerase IV
P: DNA (5'-D(*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*(DOC))-3')
B: DNA (5'-D(*TP*CP*AP*TP*(EFG)P*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3856
Polymers48,8693
Non-polymers5163
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5650 Å2
ΔGint-49 kcal/mol
Surface area20040 Å2
MethodPISA
2
J: DNA polymerase IV
K: DNA (5'-D(*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*(DOC))-3')
M: DNA (5'-D(*TP*CP*AP*TP*(EFG)P*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4097
Polymers48,8693
Non-polymers5404
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5350 Å2
ΔGint-50 kcal/mol
Surface area19820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.700, 111.419, 98.807
Angle α, β, γ (deg.)90.00, 102.57, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AJ

#1: Protein DNA polymerase IV / / Pol IV


Mass: 39977.512 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus P2 (archaea) / Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: dbh, dpo4, SSO2448 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold (DE3) / References: UniProt: Q97W02, DNA-directed DNA polymerase

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DNA chain , 2 types, 4 molecules PKBM

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


Mass: 3751.466 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Based on previously crystallization sequence.
#3: DNA chain DNA (5'-D(*TP*CP*AP*TP*(EFG)P*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*C)-3')


Mass: 5140.322 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Based on previously crystallization sequence.

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Non-polymers , 3 types, 169 molecules

#4: Chemical ChemComp-DCP / 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / Deoxycytidine triphosphate


Mass: 467.157 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16N3O13P3
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.94 Å3/Da / Density % sol: 58.14 %
Crystal growTemperature: 293 K / pH: 7.4
Details: 200 uM Dpo4, 240 uM primer-template DNA complex, 5 mM MgCl2, 1 mM dCTP, 20 mM Tris-HCl (pH 7.4), 60 mM NaCl, 2% glycerol (v/v), and 5 mM -mercaptoethanol. Precipitant: 0.1M Tris-HCl (pH 7.4) ...Details: 200 uM Dpo4, 240 uM primer-template DNA complex, 5 mM MgCl2, 1 mM dCTP, 20 mM Tris-HCl (pH 7.4), 60 mM NaCl, 2% glycerol (v/v), and 5 mM -mercaptoethanol. Precipitant: 0.1M Tris-HCl (pH 7.4), 15% polyethylene glycol 3350 (w/v), 0.1 M Ca(CH3COO)2, and 2% glycerol (v/v), temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.98
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Aug 7, 2011
RadiationMonochromator: KOHZU / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.297→30 Å / Num. obs: 48579 / % possible obs: 97.8 % / Observed criterion σ(I): 5 / Redundancy: 4.6 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 15.3
Reflection shellResolution: 2.297→2.38 Å / Redundancy: 4 % / Rmerge(I) obs: 0.534 / Mean I/σ(I) obs: 2.32 / % possible all: 85.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.6.0117phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3V6H

3v6h


Resolution: 2.3→29.84 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.913 / SU B: 15.038 / SU ML: 0.186 / Cross valid method: THROUGHOUT / σ(F): 2.297 / ESU R: 0.299 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.273 2456 5.1 %RANDOM
Rwork0.21 ---
obs0.213 48579 97.7 %-
all-48579 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.28 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å20 Å22.94 Å2
2---1.35 Å20 Å2
3---3.43 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5516 1085 61 162 6824
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0186862
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1421.9039460
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5195683
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.13823.714245
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.049151119
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2591547
X-RAY DIFFRACTIONr_chiral_restr0.1350.21026
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214635
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 152 -
Rwork0.276 2858 -
obs--83.2 %
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)
11.5602-0.0905-0.3710.6016-0.411.4473-0.0181-0.4908-0.09290.20630.0225-0.0392-0.10520.0723-0.00450.2059-0.04190.03250.2505-0.02480.09449.7247-0.250288.4575
21.70.64920.12341.3915-0.04871.0963-0.04510.2705-0.0605-0.16960.05650.0721-0.0076-0.0826-0.01130.027100.01050.0555-0.01660.09791.6055-0.916344.3398
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1J1 - 342
2X-RAY DIFFRACTION1M4 - 16
3X-RAY DIFFRACTION1K3 - 13
4X-RAY DIFFRACTION2A1 - 342
5X-RAY DIFFRACTION2B1 - 17
6X-RAY DIFFRACTION2P2 - 13

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