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- PDB-3qz7: T-3 ternary complex of Dpo4 -

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Basic information

Entry
Database: PDB / ID: 3qz7
TitleT-3 ternary complex of Dpo4
Components
  • 5'-D(*GP*GP*CP*AP*CP*TP*GP*AP*TP*CP*GP*GP*G)-3'
  • 5'-D(*TP*TP*AP*CP*GP*CP*CP*TP*CP*GP*AP*TP*CP*AP*GP*TP*GP*CP*C)-3'
  • DNA polymerase IV
KeywordsTRANSFERASE/DNA / lesion bypass / single-base deletion / -1 frameshift / REPLICATION-DNA complex / 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 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 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.998 Å
AuthorsPata, J.D. / Wu, Y. / Wilson, R.C.
CitationJournal: J.Bacteriol. / Year: 2011
Title: The y-family DNA polymerase dpo4 uses a template slippage mechanism to create single-base deletions.
Authors: Wu, Y. / Wilson, R.C. / Pata, J.D.
History
DepositionMar 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
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_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_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.pdbx_dist_value / _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_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_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
P: 5'-D(*GP*GP*CP*AP*CP*TP*GP*AP*TP*CP*GP*GP*G)-3'
T: 5'-D(*TP*TP*AP*CP*GP*CP*CP*TP*CP*GP*AP*TP*CP*AP*GP*TP*GP*CP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5787
Polymers50,9903
Non-polymers5874
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-60 kcal/mol
Surface area20180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.708, 102.461, 52.743
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 / Dpo4 / Y-family DNA polymerase / Pol IV


Mass: 41200.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: P2 / Gene: dbh, dpo4, SSO2448 / Plasmid: pKKT7 / Production host: Escherichia coli (E. coli) / Strain (production host): BLR(DE3)pLysS / 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*CP*AP*CP*TP*GP*AP*TP*CP*GP*GP*G)-3'


Mass: 4032.622 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Primer DNA strand
#3: DNA chain 5'-D(*TP*TP*AP*CP*GP*CP*CP*TP*CP*GP*AP*TP*CP*AP*GP*TP*GP*CP*C)-3'


Mass: 5756.723 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Template DNA strand

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Non-polymers , 3 types, 74 molecules

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


Mass: 467.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O13P3
#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


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.62 Å3/Da / Density % sol: 52.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 18% PEG3350, 100 mM HEPES, 100 mM calcium acetate, 2.5% glycerol, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 18, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 1.998→30 Å / Num. all: 37103 / Num. obs: 33358 / % possible obs: 89.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 32.6
Reflection shellResolution: 2→2.03 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 1.6 / Num. unique all: 586 / % possible all: 31.9

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Processing

Software
NameClassification
CBASSdata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JX4

1jx4


Resolution: 1.998→25.539 Å / SU ML: 0.28 / Isotropic thermal model: ANISOTROPIC / σ(F): 0.14 / Phase error: 27.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2668 1629 4.89 %RANDOM
Rwork0.227 ---
obs0.229 33327 90.04 %-
all-33327 --
Solvent computationShrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.986 Å2 / ksol: 0.44 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.8382 Å20 Å2-0 Å2
2---0.1002 Å20 Å2
3----3.738 Å2
Refinement stepCycle: LAST / Resolution: 1.998→25.539 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2743 572 31 70 3416
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013461
X-RAY DIFFRACTIONf_angle_d1.4614783
X-RAY DIFFRACTIONf_dihedral_angle_d19.1651373
X-RAY DIFFRACTIONf_chiral_restr0.156544
X-RAY DIFFRACTIONf_plane_restr0.004501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9981-2.05690.3237500.35411101X-RAY DIFFRACTION38
2.0569-2.12320.3333810.3171898X-RAY DIFFRACTION65
2.1232-2.19910.30821390.29232657X-RAY DIFFRACTION91
2.1991-2.28710.31571650.26472810X-RAY DIFFRACTION99
2.2871-2.39110.3051530.25072882X-RAY DIFFRACTION99
2.3911-2.5170.28081490.24532884X-RAY DIFFRACTION100
2.517-2.67460.29271350.25122919X-RAY DIFFRACTION100
2.6746-2.88080.31251470.25632896X-RAY DIFFRACTION100
2.8808-3.17020.27091650.24242917X-RAY DIFFRACTION100
3.1702-3.62790.25731410.22192967X-RAY DIFFRACTION100
3.6279-4.56650.25841530.19622969X-RAY DIFFRACTION100
4.5665-25.54120.24211510.21662798X-RAY DIFFRACTION89

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