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- PDB-4f4z: Y-family DNA polymerase chimera Dpo4-Dpo4-Dbh -

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Basic information

Entry
Database: PDB / ID: 4f4z
TitleY-family DNA polymerase chimera Dpo4-Dpo4-Dbh
Components
  • DNA (5'-D(*AP*GP*GP*GP*GP*GP*AP*AP*GP*CP*CP*G)-3')
  • DNA (5'-D(*TP*TP*CP*CP*GP*CP*CP*CP*GP*GP*CP*TP*TP*CP*CP*CP*CP*CP*T)-3')
  • DNA polymerase IV
KeywordsTRANSFERASE/DNA / Y-family polymerase / TRANSFERASE-DNA complex
Function / homology
Function and homology information


SOS response / error-prone translesion synthesis / DNA-templated DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / magnesium ion binding / cytosol
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
DNA / DNA (> 10) / DNA polymerase IV / DNA polymerase IV
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
Sulfolobus acidocaldarius (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.305 Å
AuthorsPata, J.D. / Wilson, R.C.
CitationJournal: Structure / Year: 2013
Title: Y-family polymerase conformation is a major determinant of fidelity and translesion specificity.
Authors: Wilson, R.C. / Jackson, M.A. / Pata, J.D.
History
DepositionMay 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 2, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2013Group: Database references
Revision 1.2Jan 20, 2016Group: Source and taxonomy
Revision 1.3Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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.pdbx_dist_value / _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_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
B: DNA polymerase IV
A: DNA polymerase IV
P: DNA (5'-D(*AP*GP*GP*GP*GP*GP*AP*AP*GP*CP*CP*G)-3')
T: DNA (5'-D(*TP*TP*CP*CP*GP*CP*CP*CP*GP*GP*CP*TP*TP*CP*CP*CP*CP*CP*T)-3')
C: DNA (5'-D(*AP*GP*GP*GP*GP*GP*AP*AP*GP*CP*CP*G)-3')
D: DNA (5'-D(*TP*TP*CP*CP*GP*CP*CP*CP*GP*GP*CP*TP*TP*CP*CP*CP*CP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,3079
Polymers101,1866
Non-polymers1203
Water1,63991
1
B: DNA polymerase IV
C: DNA (5'-D(*AP*GP*GP*GP*GP*GP*AP*AP*GP*CP*CP*G)-3')
D: DNA (5'-D(*TP*TP*CP*CP*GP*CP*CP*CP*GP*GP*CP*TP*TP*CP*CP*CP*CP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6735
Polymers50,5933
Non-polymers802
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-57 kcal/mol
Surface area19350 Å2
MethodPISA
2
A: DNA polymerase IV
P: DNA (5'-D(*AP*GP*GP*GP*GP*GP*AP*AP*GP*CP*CP*G)-3')
T: DNA (5'-D(*TP*TP*CP*CP*GP*CP*CP*CP*GP*GP*CP*TP*TP*CP*CP*CP*CP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6334
Polymers50,5933
Non-polymers401
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-47 kcal/mol
Surface area19520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.966, 51.196, 98.842
Angle α, β, γ (deg.)75.60, 82.97, 70.14
Int Tables number1
Space group name H-MP1

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Components

#1: Protein DNA polymerase IV / Pol IV


Mass: 41171.043 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea), (gene. exp.) Sulfolobus acidocaldarius (acidophilic)
Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2
Gene: dbh, dpo4, Dpo4 (S. solfataricus) and Dbh (S. acidocaldarius), SSO2448, Saci_05 54
Production host: Escherichia coli (E. coli) / Strain (production host): BLR(DE3)pLysS
References: UniProt: Q97W02, UniProt: Q4JB80, DNA-directed DNA polymerase
#2: DNA chain DNA (5'-D(*AP*GP*GP*GP*GP*GP*AP*AP*GP*CP*CP*G)-3')


Mass: 3777.467 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Primer DNA
#3: DNA chain DNA (5'-D(*TP*TP*CP*CP*GP*CP*CP*CP*GP*GP*CP*TP*TP*CP*CP*CP*CP*CP*T)-3')


Mass: 5644.623 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Template DNA
#4: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.32 Å3/Da / Density % sol: 46.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10% PEG-3350, 100 mM Ca(OAc)2, 100 mM HEPES, 2.5% Glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 18, 2007
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 25946 / Num. obs: 21042 / % possible obs: 81.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 21.3
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 2 / Num. unique all: 947 / % possible all: 50.5

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERin PHENIXphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.305→27.065 Å / SU ML: 0.42 / σ(F): 2.21 / Phase error: 31.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.26 1589 4.9 %
Rwork0.1847 --
obs0.1883 -80.8 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.22 Å2 / ksol: 0.328 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.1877 Å22.6214 Å22.4321 Å2
2--1.3028 Å21.8895 Å2
3----3.4905 Å2
Refinement stepCycle: LAST / Resolution: 2.305→27.065 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5440 997 3 91 6531
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076641
X-RAY DIFFRACTIONf_angle_d1.1429150
X-RAY DIFFRACTIONf_dihedral_angle_d18.2822646
X-RAY DIFFRACTIONf_chiral_restr0.0761062
X-RAY DIFFRACTIONf_plane_restr0.004987
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3046-2.3790.4181940.29251801X-RAY DIFFRACTION52
2.379-2.46390.30641060.25792211X-RAY DIFFRACTION63
2.4639-2.56250.31741270.23512449X-RAY DIFFRACTION70
2.5625-2.6790.31551320.24492532X-RAY DIFFRACTION73
2.679-2.82010.33821470.25352680X-RAY DIFFRACTION78
2.8201-2.99660.31881410.25572920X-RAY DIFFRACTION83
2.9966-3.22760.32871580.22573055X-RAY DIFFRACTION89
3.2276-3.55180.26271680.18873232X-RAY DIFFRACTION94
3.5518-4.06430.24781670.16893310X-RAY DIFFRACTION96
4.0643-5.11490.20631760.14243388X-RAY DIFFRACTION97
5.1149-27.06730.23551730.16053276X-RAY DIFFRACTION95
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)
14.9476-2.8279-1.31023.3907-1.43422.97760.07410.63-0.05910.1749-0.3853-0.64270.8397-0.50540.21990.97260.0790.13790.4733-0.09010.5342-2.24964.9568-64.9276
26.2667-2.32880.03088.70450.49565.0635-0.6105-0.705-0.93061.03840.1946-0.6221-0.45590.93610.3290.40440.0095-0.03010.99090.24480.552319.8614-2.5158-5.4759
33.6746-0.40490.93742.02-0.58064.5775-0.0455-0.01520.04950.02150.05470.2091-0.519-1.0373-0.01240.43890.1840.14250.5680.13310.4288-14.943325.71-52.7312
45.0837-2.1291-0.5298.0519-1.43196.49580.21620.68450.2186-1.33570.0678-0.36620.4069-0.6333-0.2660.68640.01460.08720.64020.15450.3716-7.811421.0595-75.4081
56.40971.93910.88863.9757-0.06522.96120.06610.10450.0744-0.1680.0235-0.18470.57770.1484-0.10840.6460.12940.09590.28910.0820.3917-0.1108-1.4773-50.0144
61.8067-0.47880.31942.20370.86443.6689-0.00850.16750.2587-0.02250.131-0.1932-0.58970.3187-0.1630.3209-0.06370.05410.38440.15710.42795.264415.7481-18.528
73.1568-1.33571.90645.05840.94596.8246-0.309-0.38-0.35360.97380.47380.44-0.1868-0.0513-0.00730.48430.01670.13290.55480.03160.3816.41037.64554.5532
87.68341.921-1.82255.67040.84153.19890.17391.0042-0.0915-0.08-0.34590.31920.013-0.60980.15080.27090.01850.06560.7686-0.00730.342425.0454-7.7146-21.0609
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN P AND RESID 2:13 ) OR ( CHAIN T AND RESID 5:17 )P2 - 13
2X-RAY DIFFRACTION1( CHAIN P AND RESID 2:13 ) OR ( CHAIN T AND RESID 5:17 )T5 - 17
3X-RAY DIFFRACTION2( CHAIN C AND RESID 2:13 ) OR ( CHAIN D AND RESID 6:17 )C2 - 13
4X-RAY DIFFRACTION2( CHAIN C AND RESID 2:13 ) OR ( CHAIN D AND RESID 6:17 )D6 - 17
5X-RAY DIFFRACTION3( CHAIN A AND RESID 1:167 )A1 - 167
6X-RAY DIFFRACTION4( CHAIN A AND RESID 168:244 )A168 - 244
7X-RAY DIFFRACTION5( CHAIN A AND RESID 245:342 )A245 - 342
8X-RAY DIFFRACTION6( CHAIN B AND RESID 1:167 )B1 - 167
9X-RAY DIFFRACTION7( CHAIN B AND RESID 168:244 )B168 - 244
10X-RAY DIFFRACTION8( CHAIN B AND RESID 245:341 )B245 - 341

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