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- PDB-4f4x: Y-family DNA polymerase chimera Dbh-Dpo4-Dpo4 #2 -

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Basic information

Entry
Database: PDB / ID: 4f4x
TitleY-family DNA polymerase chimera Dbh-Dpo4-Dpo4 #2
Components
  • DNA (5'-D(*GP*GP*CP*AP*CP*TP*GP*AP*TP*CP*GP*GP*GP*C)-3')
  • DNA (5'-D(*TP*TP*AP*CP*GP*CP*CP*CP*TP*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


error-prone translesion synthesis / DNA-templated DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA repair / 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 / DNA polymerase IV
Similarity search - Component
Biological speciesSulfolobus acidocaldarius (acidophilic)
Sulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.049 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 1.2Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Feb 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*GP*C)-3')
T: DNA (5'-D(*TP*TP*AP*CP*GP*CP*CP*CP*TP*GP*AP*TP*CP*AP*GP*TP*GP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8318
Polymers51,2033
Non-polymers6275
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6280 Å2
ΔGint-79 kcal/mol
Surface area20020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.122, 102.306, 52.879
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 / / Pol IV


Mass: 41124.742 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 (S. solfataricus) and Dbh (S. acidocaldarius), Saci_0554, dpo4, 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, 2 molecules PT

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


Mass: 4321.803 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically synthesized
#3: DNA chain DNA (5'-D(*TP*TP*AP*CP*GP*CP*CP*CP*TP*GP*AP*TP*CP*AP*GP*TP*GP*CP*C)-3')


Mass: 5756.723 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically synthesized

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Non-polymers , 3 types, 191 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-DCP / 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / Deoxycytidine triphosphate


Mass: 467.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O13P3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.67 Å3/Da / Density % sol: 53.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 10% PEG-3350, 100 mM Ca(OAc)2, 100 mM MES/Tris, 2.5% Glycerol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 7, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.04→30 Å / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 24.4
Reflection shellResolution: 2.04→2.08 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.333 / Mean I/σ(I) obs: 5.1 / Num. unique all: 1401 / % possible all: 80.9

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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: 2.049→29.735 Å / SU ML: 0.38 / σ(F): 1.33 / Phase error: 26.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2503 1760 5.01 %
Rwork0.2181 --
obs0.2196 35101 99.66 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.756 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-12.7286 Å2-0 Å2-0 Å2
2---4.7188 Å20 Å2
3----8.0098 Å2
Refinement stepCycle: LAST / Resolution: 2.049→29.735 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2738 651 32 186 3607
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083584
X-RAY DIFFRACTIONf_angle_d1.3234980
X-RAY DIFFRACTIONf_dihedral_angle_d18.2681456
X-RAY DIFFRACTIONf_chiral_restr0.072569
X-RAY DIFFRACTIONf_plane_restr0.006521
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0495-2.10490.41691310.37132467X-RAY DIFFRACTION98
2.1049-2.16680.38781320.36432509X-RAY DIFFRACTION99
2.1668-2.23670.35721350.34812523X-RAY DIFFRACTION99
2.2367-2.31660.41821290.3392527X-RAY DIFFRACTION100
2.3166-2.40930.37441350.2862557X-RAY DIFFRACTION100
2.4093-2.51890.33521320.27162551X-RAY DIFFRACTION100
2.5189-2.65160.27471370.24262538X-RAY DIFFRACTION100
2.6516-2.81770.26391360.22712557X-RAY DIFFRACTION100
2.8177-3.0350.25611330.20852551X-RAY DIFFRACTION100
3.035-3.34010.22731370.2022597X-RAY DIFFRACTION100
3.3401-3.82250.2371380.19182587X-RAY DIFFRACTION100
3.8225-4.81270.20881420.17172630X-RAY DIFFRACTION100
4.8127-29.73850.1881430.19682747X-RAY DIFFRACTION100
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)
10.0355-0.0020.03680.00440.00040.03830.04450.042-0.0697-0.0302-0.01360.06760.02460.01480.07780.3229-0.13630.08870.15590.1780.161731.4215-28.0889-1.5257
20.0634-0.03940.04450.029-0.0330.04420.08050.06440.0765-0.1826-0.08520.1223-0.00580.1082-0.00390.13240.0059-0.02190.1727-0.01680.211222.3512-7.7427-19.0497
30.00520.00640.00340.00910.00370.00180.03220.0238-0.04980.0050.01440.00710.0517-0.0003-0.00010.3284-0.1140.02750.3003-0.11310.407215.9213-34.3538-17.5807
40.00190-0.0027-0.00020.00060.002-0.0273-0.0015-0.00330.016-0.00740.02350.024-0.0009-00.2428-0.06540.04910.322-0.01540.215615.9441-19.1376-4.0459
50.01120.00490.00170.0132-0.01070.01060.02740.01430.01670.1065-0.0675-0.043-0.04810.0523-0.00030.18520.0208-0.02630.21660.01710.182643.9992-17.80372.4849
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN P AND RESID 1:14 ) OR ( CHAIN T AND RESID 2:19 )P1 - 14
2X-RAY DIFFRACTION1( CHAIN P AND RESID 1:14 ) OR ( CHAIN T AND RESID 2:19 )T2 - 19
3X-RAY DIFFRACTION2( CHAIN A AND RESID 1:168 )A1 - 168
4X-RAY DIFFRACTION3( CHAIN A AND RESID 169:231 )A169 - 231
5X-RAY DIFFRACTION4( CHAIN A AND RESID 232:246 )A232 - 246
6X-RAY DIFFRACTION5( CHAIN A AND RESID 247:342 )A247 - 342

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