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- PDB-4f4w: Y-family DNA polymerase chimera Dbh-Dpo4-Dpo4 #1 -

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Basic information

Entry
Database: PDB / ID: 4f4w
TitleY-family DNA polymerase chimera Dbh-Dpo4-Dpo4 #1
Components
  • DNA (5'-D(*GP*GP*CP*AP*CP*TP*GP*AP*TP*CP*GP*GP*C)-3')
  • DNA (5'-D(*TP*TP*AP*CP*GP*GP*CP*CP*GP*AP*TP*CP*AP*GP*TP*GP*CP*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
2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / 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: 1.898 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_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
A: DNA polymerase IV
P: DNA (5'-D(*GP*GP*CP*AP*CP*TP*GP*AP*TP*CP*GP*GP*C)-3')
T: DNA (5'-D(*TP*TP*AP*CP*GP*GP*CP*CP*GP*AP*TP*CP*AP*GP*TP*GP*CP*C)-3')
B: DNA polymerase IV
E: DNA (5'-D(*GP*GP*CP*AP*CP*TP*GP*AP*TP*CP*GP*GP*C)-3')
F: DNA (5'-D(*TP*TP*AP*CP*GP*GP*CP*CP*GP*AP*TP*CP*AP*GP*TP*GP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,31412
Polymers101,2206
Non-polymers1,0956
Water12,755708
1
A: DNA polymerase IV
P: DNA (5'-D(*GP*GP*CP*AP*CP*TP*GP*AP*TP*CP*GP*GP*C)-3')
T: DNA (5'-D(*TP*TP*AP*CP*GP*GP*CP*CP*GP*AP*TP*CP*AP*GP*TP*GP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1576
Polymers50,6103
Non-polymers5473
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5190 Å2
ΔGint-58 kcal/mol
Surface area19700 Å2
MethodPISA
2
B: DNA polymerase IV
E: DNA (5'-D(*GP*GP*CP*AP*CP*TP*GP*AP*TP*CP*GP*GP*C)-3')
F: DNA (5'-D(*TP*TP*AP*CP*GP*GP*CP*CP*GP*AP*TP*CP*AP*GP*TP*GP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1576
Polymers50,6103
Non-polymers5473
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint-56 kcal/mol
Surface area19870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.820, 99.655, 101.625
Angle α, β, γ (deg.)90.00, 90.16, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein DNA polymerase IV / / Pol IV


Mass: 41124.742 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius (acidophilic), (gene. exp.) Sulfolobus solfataricus (archaea)
Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2
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

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DNA chain , 2 types, 4 molecules PETF

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


Mass: 3992.598 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Primer DNA
#3: DNA chain DNA (5'-D(*TP*TP*AP*CP*GP*GP*CP*CP*GP*AP*TP*CP*AP*GP*TP*GP*CP*C)-3')


Mass: 5492.554 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Template DNA

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Non-polymers , 3 types, 714 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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 708 / 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: 2.64 Å3/Da / Density % sol: 53.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: 10% PEG-3350, 100 mM Ca(OAc)2, 100 mM MES/Tris, 2.5% Glycerol, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 6, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.898→30 Å / Num. all: 83084 / Num. obs: 80176 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.039 / Net I/σ(I): 28.5
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.166 / Mean I/σ(I) obs: 3.8 / Num. unique all: 3345 / % possible all: 81.1

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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: 1.898→28.014 Å / SU ML: 0.25 / σ(F): 1.54 / Phase error: 21.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2189 1927 2.4 %
Rwork0.1865 --
obs0.1873 80155 96.52 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.2 Å2 / ksol: 0.385 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.1495 Å20 Å2-0.2172 Å2
2--6.1347 Å20 Å2
3----1.9852 Å2
Refinement stepCycle: LAST / Resolution: 1.898→28.014 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5476 1142 60 708 7386
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116946
X-RAY DIFFRACTIONf_angle_d1.4939617
X-RAY DIFFRACTIONf_dihedral_angle_d18.2282801
X-RAY DIFFRACTIONf_chiral_restr0.0791098
X-RAY DIFFRACTIONf_plane_restr0.0061023
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.898-1.94580.24841240.2194854X-RAY DIFFRACTION83
1.9458-1.99830.26021290.20495374X-RAY DIFFRACTION94
1.9983-2.05710.20341380.19455456X-RAY DIFFRACTION95
2.0571-2.12350.24281400.19375562X-RAY DIFFRACTION96
2.1235-2.19940.24051310.19485606X-RAY DIFFRACTION97
2.1994-2.28740.20151390.20035606X-RAY DIFFRACTION97
2.2874-2.39140.28221310.20095637X-RAY DIFFRACTION98
2.3914-2.51750.2431420.20045670X-RAY DIFFRACTION98
2.5175-2.67510.291390.20095692X-RAY DIFFRACTION99
2.6751-2.88140.27441350.20845712X-RAY DIFFRACTION99
2.8814-3.1710.20051390.19875770X-RAY DIFFRACTION99
3.171-3.6290.21331430.18135752X-RAY DIFFRACTION99
3.629-4.5690.1841480.15865788X-RAY DIFFRACTION99
4.569-28.01710.19431490.17545749X-RAY DIFFRACTION98

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