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- PDB-4f50: Y-family DNA polymerase chimera Dbh-Dbh-Dpo4 -

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Basic information

Entry
Database: PDB / ID: 4f50
TitleY-family DNA polymerase chimera Dbh-Dbh-Dpo4
Components
  • DNA (5'-D(*CP*CP*GP*CP*CP*T*GP*GP*CP*TP*TP*CP*CP*C)-3')
  • DNA (5'-D(*GP*GP*GP*AP*AP*GP*CP*CP*GP*GP*C)-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 acidocaldarius (acidophilic)
Sulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.215 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 29, 2014Group: Source and taxonomy
Revision 1.3Feb 12, 2014Group: Source and taxonomy
Revision 1.4Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.5Feb 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_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: DNA (5'-D(*GP*GP*GP*AP*AP*GP*CP*CP*GP*GP*C)-3')
T: DNA (5'-D(*CP*CP*GP*CP*CP*T*GP*GP*CP*TP*TP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6524
Polymers48,6123
Non-polymers401
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-33 kcal/mol
Surface area20260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.482, 124.482, 70.474
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-510-

HOH

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Components

#1: Protein DNA polymerase IV / Pol IV


Mass: 41018.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius (acidophilic), (gene. exp.) Sulfolobus solfataricus (archaea)
Strain: ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770
Gene: dbh, dpo4, Dpo4 (S. solfataricus) and Dbh (S. acidocaldarius), Saci_0554, SSO24 48
Production host: Escherichia coli (E. coli) / Strain (production host): BLR(DE3)pLysS
References: UniProt: Q4JB80, UniProt: Q97W02, DNA-directed DNA polymerase
#2: DNA chain DNA (5'-D(*GP*GP*GP*AP*AP*GP*CP*CP*GP*GP*C)-3')


Mass: 3424.236 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Primer DNA
#3: DNA chain DNA (5'-D(*CP*CP*GP*CP*CP*T*GP*GP*CP*TP*TP*CP*CP*C)-3')


Mass: 4168.692 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Template DNA
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.81 Å3/Da / Density % sol: 56.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 10% PEG-3350, 100 mM Ca(OAc)2, 100 mM HEPES, 2.5% Glycerol, pH 7.1, 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: 2.215→30 Å / Num. all: 28140 / Num. obs: 27408 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.7 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 31.9
Reflection shellResolution: 2.22→2.26 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1092 / % possible all: 79.9

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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: 2.215→28.468 Å / SU ML: 0.32 / σ(F): 1.49 / Phase error: 28.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2691 1365 4.99 %Random
Rwork0.2117 ---
obs0.2145 27377 97.41 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.503 Å2 / ksol: 0.331 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.2801 Å20 Å2-0 Å2
2--5.2801 Å20 Å2
3----10.5602 Å2
Refinement stepCycle: LAST / Resolution: 2.215→28.468 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2693 466 1 74 3234
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083254
X-RAY DIFFRACTIONf_angle_d1.2274474
X-RAY DIFFRACTIONf_dihedral_angle_d18.7691287
X-RAY DIFFRACTIONf_chiral_restr0.075512
X-RAY DIFFRACTIONf_plane_restr0.005491
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.215-2.29390.3221100.30622190X-RAY DIFFRACTION83
2.2939-2.38570.35831360.30752522X-RAY DIFFRACTION97
2.3857-2.49430.37471370.29072604X-RAY DIFFRACTION99
2.4943-2.62570.3351350.27762620X-RAY DIFFRACTION99
2.6257-2.79010.36611390.272621X-RAY DIFFRACTION99
2.7901-3.00530.3031390.24422633X-RAY DIFFRACTION100
3.0053-3.30730.30281390.21332668X-RAY DIFFRACTION100
3.3073-3.78490.26161410.19592675X-RAY DIFFRACTION100
3.7849-4.76490.2111430.16852718X-RAY DIFFRACTION100
4.7649-28.47070.23781460.19062761X-RAY DIFFRACTION97
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)
10.2579-0.63280.04083.19860.1794-0.00840.03340.63330.04140.13740.0081-0.62120.15310.08680.00070.97250.2848-0.01720.5375-0.15020.6557-27.09362.0114-14.7811
20.93980.3095-0.76984.0786-0.14514.08440.0116-0.1221-0.12990.91080.4240.20720.0937-0.1675-0.26420.4410.16670.11140.41030.05930.3495-36.3451-24.1286-15.9354
33.3590.1743-0.53643.2475-0.52933.1603-0.2975-0.48840.4511.82270.2211-0.1879-0.34590.32620.11951.42490.2679-0.12390.5594-0.03630.4967-29.3451-8.05052.3041
41.71180.28570.16973.8364-2.54826.0726-0.53761.16831.0738-0.04860.91031.1076-0.231-0.9642-0.47011.06350.0176-0.04351.22460.57470.915-43.07883.015-29.8541
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN P AND RESID 1:11 ) OR ( CHAIN T AND RESID 1:14 )P1 - 11
2X-RAY DIFFRACTION1( CHAIN P AND RESID 1:11 ) OR ( CHAIN T AND RESID 1:14 )T1 - 14
3X-RAY DIFFRACTION2( CHAIN A AND RESID 1:168 )A1 - 168
4X-RAY DIFFRACTION3( CHAIN A AND RESID 169:246 )A169 - 246
5X-RAY DIFFRACTION4( CHAIN A AND RESID 247:342 )A247 - 342

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