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Basic information

Entry
Database: PDB / ID: 4b9n
TitleStructure of the high fidelity DNA polymerase I correctly bypassing the oxidative formamidopyrimidine-dA DNA lesion.
Components
  • 5'-D(*CP*AP*AP*(FAX)*AP*GP*AP*GP*TP*CP*AP*GP*GP*CP*TP)-3'
  • 5'-D(*GP*CP*CP*TP*GP*AP*CP*TP*CP*TP*TP*TP*TP)-3'
  • DNA POLYMERASE
KeywordsTRANSFERASE/DNA / TRANSFERASE-DNA COMPLEX / OXIDATIVE DNA LESION / DNA DAMAGE / TRANS LESION SYNTHESIS
Function / homology
Function and homology information


3'-5' exonuclease activity / DNA-templated DNA replication / double-strand break repair / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding / metal ion binding
Similarity search - Function
DNA polymerase I, ribonuclease H-like domain / Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / DNA polymerase 1 / Alpha-Beta Plaits - #370 / 3'-5' exonuclease / 3'-5' exonuclease domain / DNA polymerase A / DNA polymerase family A / DNA-directed DNA polymerase, family A, conserved site ...DNA polymerase I, ribonuclease H-like domain / Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / DNA polymerase 1 / Alpha-Beta Plaits - #370 / 3'-5' exonuclease / 3'-5' exonuclease domain / DNA polymerase A / DNA polymerase family A / DNA-directed DNA polymerase, family A, conserved site / DNA polymerase family A signature. / DNA-directed DNA polymerase, family A, palm domain / DNA polymerase A domain / 5' to 3' exonuclease, C-terminal subdomain / Ribonuclease H-like superfamily/Ribonuclease H / DNA polymerase; domain 1 / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Alpha-Beta Plaits / DNA/RNA polymerase superfamily / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
sucrose / DNA / DNA (> 10) / DNA polymerase I
Similarity search - Component
Biological speciesGEOBACILLUS STEAROTHERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsGehrke, T.H. / Lischke, U. / Arnold, S. / Schneider, S. / Carell, T.
CitationJournal: Nat.Chem.Biol. / Year: 2013
Title: Unexpected Non-Hoogsteen-Based Mutagenicity Mechanism of Fapy-DNA Lesions.
Authors: Gehrke, T.H. / Lischke, U. / Gasteiger, K.L. / Schneider, S. / Arnold, S. / Muller, H.C. / Stephenson, D.S. / Zipse, H. / Carell, T.
History
DepositionSep 5, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references / Structure summary
Revision 1.2May 29, 2013Group: Database references
Revision 1.3Jul 3, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_asym.entity_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA POLYMERASE
B: 5'-D(*GP*CP*CP*TP*GP*AP*CP*TP*CP*TP*TP*TP*TP)-3'
C: 5'-D(*CP*AP*AP*(FAX)*AP*GP*AP*GP*TP*CP*AP*GP*GP*CP*TP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,84510
Polymers78,9983
Non-polymers8477
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6490 Å2
ΔGint-92.2 kcal/mol
Surface area27760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.452, 93.726, 105.265
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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DNA chain , 2 types, 2 molecules BC

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


Mass: 3908.545 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) GEOBACILLUS STEAROTHERMOPHILUS (bacteria)
#3: DNA chain 5'-D(*CP*AP*AP*(FAX)*AP*GP*AP*GP*TP*CP*AP*GP*GP*CP*TP)-3'


Mass: 4643.079 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) GEOBACILLUS STEAROTHERMOPHILUS (bacteria)

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein DNA POLYMERASE


Mass: 70446.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GEOBACILLUS STEAROTHERMOPHILUS (bacteria)
Plasmid: PDEST007 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: E1C9K5, DNA-directed DNA polymerase
#4: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 3 types, 247 molecules

#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsRESI 1-3 IN CHAIN B ARE DISORDERED RESI 1 AND 13-15 IN CHAIN C ARE DISORDERED

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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: 2.82 Å3/Da / Density % sol: 56.34 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 18, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→45.89 Å / Num. obs: 45055 / % possible obs: 99.8 % / Observed criterion σ(I): 1.5 / Redundancy: 4.9 % / Biso Wilson estimate: 28.48 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 16
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 3.2 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4B9M

4b9m


Resolution: 2.2→45.892 Å / SU ML: 0.5 / σ(F): 1.14 / Phase error: 22.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2173 4282 5 %
Rwork0.1832 --
obs0.1849 44989 99.74 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.497 Å2 / ksol: 0.36 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-14.5147 Å20 Å20 Å2
2---7.9063 Å20 Å2
3----6.6083 Å2
Refinement stepCycle: LAST / Resolution: 2.2→45.892 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4660 433 49 241 5383
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065310
X-RAY DIFFRACTIONf_angle_d0.9937275
X-RAY DIFFRACTIONf_dihedral_angle_d16.732064
X-RAY DIFFRACTIONf_chiral_restr0.065819
X-RAY DIFFRACTIONf_plane_restr0.004862
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2003-2.22530.29311350.25412599X-RAY DIFFRACTION94
2.2253-2.25150.29961410.26182700X-RAY DIFFRACTION100
2.2515-2.27890.27021440.23952730X-RAY DIFFRACTION100
2.2789-2.30780.26811410.22662732X-RAY DIFFRACTION100
2.3078-2.33820.28521390.2252713X-RAY DIFFRACTION100
2.3382-2.37020.26911440.22682649X-RAY DIFFRACTION100
2.3702-2.4040.25461500.22062758X-RAY DIFFRACTION100
2.404-2.43990.25641460.22072700X-RAY DIFFRACTION100
2.4399-2.4780.25261440.21712702X-RAY DIFFRACTION100
2.478-2.51870.23721490.20812738X-RAY DIFFRACTION100
2.5187-2.56210.23081430.20762688X-RAY DIFFRACTION100
2.5621-2.60870.24211490.21662721X-RAY DIFFRACTION100
2.6087-2.65890.27331320.21052711X-RAY DIFFRACTION100
2.6589-2.71310.24351490.20562690X-RAY DIFFRACTION100
2.7131-2.77210.21271410.19762758X-RAY DIFFRACTION100
2.7721-2.83660.24791460.19132682X-RAY DIFFRACTION100
2.8366-2.90750.2351380.1992723X-RAY DIFFRACTION100
2.9075-2.98610.26321350.21172716X-RAY DIFFRACTION100
2.9861-3.0740.24121520.19952726X-RAY DIFFRACTION100
3.074-3.17320.2221480.19632686X-RAY DIFFRACTION100
3.1732-3.28650.28611400.19462748X-RAY DIFFRACTION100
3.2865-3.41810.22371420.17632694X-RAY DIFFRACTION100
3.4181-3.57360.19521530.16572702X-RAY DIFFRACTION100
3.5736-3.76190.17821350.15492714X-RAY DIFFRACTION100
3.7619-3.99750.1751380.14762723X-RAY DIFFRACTION100
3.9975-4.30590.14251420.13522719X-RAY DIFFRACTION100
4.3059-4.73880.16131450.13452722X-RAY DIFFRACTION100
4.7388-5.42360.17221410.15322715X-RAY DIFFRACTION100
5.4236-6.82960.22121380.19572718X-RAY DIFFRACTION100
6.8296-45.90160.20731420.1712706X-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)
11.6153-0.88540.16781.7226-0.22361.3019-0.1509-0.3771-0.05180.36780.20990.0128-0.0497-0.0501-0.0180.2290.02950.02120.22530.00570.1659-10.3732-18.368854.6537
20.9202-0.36680.00731.2114-0.29980.9701-0.0073-0.0603-0.08330.05730.02240.0260.09370.00480.00180.1409-0.00210.00310.17970.00510.1837-8.6527-19.158640.1719
30.61630.35531.19520.74620.79382.3670.0251-0.05480.083-0.5108-0.01260.0701-0.109-0.38960.08380.4755-0.0534-0.05840.36370.00970.263-39.3584-7.78110.4487
41.09480.0281-0.1761.163-0.04920.51870.10030.06560.0517-0.1601-0.05270.2908-0.0662-0.1421-0.03160.18330.0044-0.010.2081-0.02530.2221-22.186-0.246529.0199
51.6517-0.42180.88370.4206-0.06951.56610.15690.1557-0.233-0.15540.04030.23540.2197-0.0581-0.10930.1858-0.0188-0.06010.1619-0.00190.208-6.7987-0.59843.4137
60.9374-0.4215-0.21681.0825-0.31510.68130.10070.0615-0.0085-0.2077-0.05270.00610.00110.0411-0.04860.1471-0.00120.00570.1564-0.00270.1462-3.4991-4.131720.0295
72.45990.37181.25474.23951.3422.15850.07880.50320.24-0.36020.1935-0.0645-0.1298-0.0108-0.13670.36160.0381-0.00060.26880.01520.2213-22.021911.139525.0263
81.50780.3748-1.33982.1945-2.03415.34090.0451-0.269-0.07990.113-0.0974-0.02910.38570.38330.17181.0674-0.21350.0340.90430.42710.6557-30.3196-25.927922.6905
92.0445-0.2855-0.25490.8297-0.91651.2675-0.1152-0.20940.5546-0.3950.1011-0.58730.2089-0.01030.03810.3826-0.05430.00730.3947-0.02040.4925-24.9867-9.311615.1868
101.13560.00290.99012.5081-0.2561.8706-0.0084-0.13250.1816-0.5954-0.0128-0.27191.058-0.2204-0.05230.4176-0.04610.06430.3814-0.00050.3732-22.5793-13.312820.5744
111.18720.0530.20541.1481-0.77821.4119-0.0754-0.0955-0.6744-0.20160.072-0.0360.4661-0.14650.06510.986-0.4742-0.22780.64240.29490.7373-38.3767-25.841619.5697
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 297:368)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 369:494)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 495:585)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 586:654)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 655:732)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 733:868)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 869:876)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 1:4)
9X-RAY DIFFRACTION9(CHAIN B AND RESID 5:11)
10X-RAY DIFFRACTION10(CHAIN C AND RESID 4:10)
11X-RAY DIFFRACTION11(CHAIN C AND RESID 11:14)

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