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- PDB-4f4y: Y-family DNA polymerase chimera Dbh-Dpo4-Dbh -

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Basic information

Entry
Database: PDB / ID: 4f4y
TitleY-family DNA polymerase chimera Dbh-Dpo4-Dbh
Components
  • DNA (5'-D(*GP*GP*CP*AP*CP*TP*GP*AP*TP*CP*GP*GP*GP*CP*CP*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 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: 2.338 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_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
B: DNA polymerase IV
C: DNA (5'-D(*GP*GP*CP*AP*CP*TP*GP*AP*TP*CP*GP*GP*GP*CP*CP*C)-3')
D: DNA (5'-D(*TP*TP*AP*CP*GP*CP*CP*CP*TP*GP*AP*TP*CP*AP*GP*TP*GP*CP*C)-3')
P: DNA (5'-D(*GP*GP*CP*AP*CP*TP*GP*AP*TP*CP*GP*GP*GP*CP*CP*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)104,59812
Polymers103,5046
Non-polymers1,0956
Water4,540252
1
A: DNA polymerase IV
P: DNA (5'-D(*GP*GP*CP*AP*CP*TP*GP*AP*TP*CP*GP*GP*GP*CP*CP*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)52,2996
Polymers51,7523
Non-polymers5473
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6250 Å2
ΔGint-65 kcal/mol
Surface area20080 Å2
MethodPISA
2
B: DNA polymerase IV
C: DNA (5'-D(*GP*GP*CP*AP*CP*TP*GP*AP*TP*CP*GP*GP*GP*CP*CP*C)-3')
D: 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)52,2996
Polymers51,7523
Non-polymers5473
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6180 Å2
ΔGint-69 kcal/mol
Surface area20380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.076, 103.390, 112.988
Angle α, β, γ (deg.)90.00, 101.76, 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: 41094.938 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 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, 4 molecules CPDT

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


Mass: 4900.167 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Details: Chemically synthesized

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Non-polymers , 3 types, 258 molecules

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


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2.93 Å3/Da / Density % sol: 58.05 %
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, 250mM sucrose, 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: 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: 2.338→30 Å / Num. all: 49979 / Num. obs: 47630 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 16.5
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.245 / Mean I/σ(I) obs: 3.9 / Num. unique all: 2002 / % possible all: 80.7

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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: 2.338→29.25 Å / SU ML: 0.43 / σ(F): 1.53 / Phase error: 30.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2586 1890 3.97 %
Rwork0.2219 --
obs0.2234 47570 94.1 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.651 Å2 / ksol: 0.386 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--9.1291 Å2-0 Å25.8228 Å2
2---8.0482 Å20 Å2
3---17.1773 Å2
Refinement stepCycle: LAST / Resolution: 2.338→29.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5460 1378 52 252 7142
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067133
X-RAY DIFFRACTIONf_angle_d1.119912
X-RAY DIFFRACTIONf_dihedral_angle_d19.0752868
X-RAY DIFFRACTIONf_chiral_restr0.0631149
X-RAY DIFFRACTIONf_plane_restr0.0041017
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3382-2.40140.36121100.29982597X-RAY DIFFRACTION70
2.4014-2.4720.38131400.32293299X-RAY DIFFRACTION89
2.472-2.55170.37521370.29713430X-RAY DIFFRACTION92
2.5517-2.64290.32341520.30113520X-RAY DIFFRACTION94
2.6429-2.74860.34761480.293470X-RAY DIFFRACTION94
2.7486-2.87360.37961480.28783558X-RAY DIFFRACTION96
2.8736-3.0250.33641480.24643609X-RAY DIFFRACTION97
3.025-3.21430.25351510.22123665X-RAY DIFFRACTION99
3.2143-3.46210.25611560.21363661X-RAY DIFFRACTION98
3.4621-3.80980.25031470.21153702X-RAY DIFFRACTION98
3.8098-4.35960.20951570.17943682X-RAY DIFFRACTION99
4.3596-5.48670.21561500.18193719X-RAY DIFFRACTION99
5.4867-29.25190.18291460.20053768X-RAY DIFFRACTION99
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)
11.0779-1.2214-0.36351.44750.42540.3858-0.1145-0.02120.28320.1395-0.0192-0.1511-0.22810.0252-0.01150.32550.23070.09390.1634-0.03070.6955-9.513127.258251.4019
21.2112.1571-0.07743.8401-0.13720.0053-0.33860.16030.0278-0.40470.0520.0789-0.06240.02460.26520.4049-0.10730.04040.50680.02380.44712.263525.4074109.424
31.783-0.0288-0.49141.54310.5472.6027-0.0513-0.2837-0.09470.2131-0.12750.05280.13440.130.17160.2373-0.0156-0.04140.25770.05730.1938.87285.844659.0978
41.16630.21550.46033.1044-0.9741.7643-0.07830.0120.64760.00330.0061-0.5076-0.54570.32970.0880.8803-0.24980.04640.4885-0.15570.87526.814131.841367.5836
55.4270.515-2.26711.11130.93383.66640.02320.07310.2462-0.0192-0.0390.0021-0.14240.0770.03460.19510.0168-0.04170.16880.03030.1998-12.57717.242438.3027
61.3133-0.0651-0.16251.2171-0.14592.2618-0.10310.1669-0.011-0.2489-0.0665-0.00420.1993-0.08350.16580.3129-0.0251-0.03030.3871-0.04010.1946-17.1372.4402106.5134
71.1165-0.93910.09533.44040.92631.1287-0.1410.00160.661-0.16270.00590.367-0.5947-0.17520.12890.80120.1269-0.03350.53760.06160.8842-15.575127.686395.3046
83.8306-0.637-1.97881.84770.41913.4022-0.05080.28920.1138-0.1118-0.03430.0233-0.13530.01720.07560.1937-0.0362-0.06350.3580.01810.17554.161416.07125.8771
90.9533-0.4540.85750.2149-0.40710.7703-0.0627-0.13690.28340.0580.0749-0.0565-0.28770.26250.00260.3717-0.05230.08450.3795-0.01910.468-6.249916.336266.3877
101.20010.5505-0.47091.42981.35512.2869-0.25450.24330.4809-0.22960.12290.1567-0.6344-0.34660.13470.45450.1009-0.00490.57720.03760.4757-1.96712.08698.0688
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN P AND RESID 1:16 ) OR ( CHAIN T AND RESID 2:19 )P1 - 16
2X-RAY DIFFRACTION1( CHAIN P AND RESID 1:16 ) OR ( CHAIN T AND RESID 2:19 )T2 - 19
3X-RAY DIFFRACTION2( CHAIN C AND RESID 1:16 )C1 - 16
4X-RAY DIFFRACTION3( CHAIN A AND RESID 1:169 )A1 - 169
5X-RAY DIFFRACTION4( CHAIN A AND RESID 170:231 )A170 - 231
6X-RAY DIFFRACTION5( CHAIN A AND RESID 247:343 )A247 - 343
7X-RAY DIFFRACTION6( CHAIN B AND RESID 1:169 )B1 - 169
8X-RAY DIFFRACTION7( CHAIN B AND RESID 170:231 )B170 - 231
9X-RAY DIFFRACTION8( CHAIN B AND RESID 247:343 )B247 - 343
10X-RAY DIFFRACTION9( CHAIN A AND RESID 232:246 )A232 - 246
11X-RAY DIFFRACTION10( CHAIN B AND RESID 232:246 )B232 - 246

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