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- PDB-4b9l: Structure of the high fidelity DNA polymerase I with the oxidativ... -

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Basic information

Entry
Database: PDB / ID: 4b9l
TitleStructure of the high fidelity DNA polymerase I with the oxidative formamidopyrimidine-dA DNA lesion in the pre-insertion site.
Components
  • 5'-D(*CP*AP*GP*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)-3'
  • DNA POLYMERASE I
KeywordsTRANSFERASE/DNA / TRANSFERASE-DNA COMPLEX / OXIDATIVE DNA LESION / DNA DAMAGE / TRANS LESION SYNTHESIS / REPLICATION
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 / DNA polymerase 1 / Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / Alpha-Beta Plaits - #370 / 3'-5' exonuclease / 3'-5' exonuclease domain / DNA polymerase A / DNA polymerase family A ...: / DNA polymerase I, ribonuclease H-like domain / DNA polymerase 1 / Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / 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: 2.05 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.ptnr2_label_asym_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 I
B: 5'-D(*GP*CP*CP*TP*GP*AP*CP*TP*CP*TP)-3'
C: 5'-D(*CP*AP*GP*FAX*AP*GP*AP*GP*TP*CP*AP*GP*GP*CP*TP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,8529
Polymers78,1023
Non-polymers7516
Water4,089227
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6380 Å2
ΔGint-70.4 kcal/mol
Surface area27400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.528, 93.265, 106.107
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)-3'


Mass: 2995.967 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) GEOBACILLUS STEAROTHERMOPHILUS (bacteria)
#3: DNA chain 5'-D(*CP*AP*GP*FAX*AP*GP*AP*GP*TP*CP*AP*GP*GP*CP*TP)-3'


Mass: 4659.078 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 I


Mass: 70446.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GEOBACILLUS STEAROTHERMOPHILUS (bacteria)
Description: GERMAN COLLECTION OF MICROORGANISMS DSM NO. 22 / 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, 232 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsCHAIN C RESIDUES 1-3 AND 15 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: 2.87 Å3/Da / Density % sol: 56.84 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 26, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→45.37 Å / Num. obs: 55071 / % possible obs: 99.8 % / Observed criterion σ(I): 1.5 / Redundancy: 4.2 % / Biso Wilson estimate: 25.35 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 6.6
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.4 / % possible all: 100

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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 1U45

1u45


Resolution: 2.05→41.156 Å / SU ML: 0.5 / σ(F): 0 / Phase error: 22.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2256 2758 5 %
Rwork0.1886 --
obs0.1905 54997 99.74 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.224 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-10.9087 Å20 Å20 Å2
2---3.1645 Å20 Å2
3----7.7442 Å2
Refinement stepCycle: LAST / Resolution: 2.05→41.156 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4653 432 44 227 5356
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095293
X-RAY DIFFRACTIONf_angle_d1.2127257
X-RAY DIFFRACTIONf_dihedral_angle_d17.612057
X-RAY DIFFRACTIONf_chiral_restr0.078821
X-RAY DIFFRACTIONf_plane_restr0.005863
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.08540.28491400.26072585X-RAY DIFFRACTION100
2.0854-2.12330.34521370.23942555X-RAY DIFFRACTION100
2.1233-2.16410.25861410.23072591X-RAY DIFFRACTION100
2.1641-2.20830.24311310.21472591X-RAY DIFFRACTION100
2.2083-2.25630.28271460.20592572X-RAY DIFFRACTION100
2.2563-2.30880.23591300.19542588X-RAY DIFFRACTION100
2.3088-2.36650.28191310.19942605X-RAY DIFFRACTION100
2.3665-2.43050.25081440.20572550X-RAY DIFFRACTION100
2.4305-2.5020.24861270.19832627X-RAY DIFFRACTION100
2.502-2.58270.24641420.2032583X-RAY DIFFRACTION100
2.5827-2.6750.251390.19572596X-RAY DIFFRACTION100
2.675-2.78210.23911340.20452605X-RAY DIFFRACTION100
2.7821-2.90870.25571370.20022615X-RAY DIFFRACTION100
2.9087-3.0620.24061360.21522614X-RAY DIFFRACTION100
3.062-3.25380.23361360.20092617X-RAY DIFFRACTION100
3.2538-3.50490.20731400.18182624X-RAY DIFFRACTION100
3.5049-3.85740.2051370.16592632X-RAY DIFFRACTION100
3.8574-4.4150.17131400.1492662X-RAY DIFFRACTION100
4.415-5.56020.18381410.15352672X-RAY DIFFRACTION100
5.5602-41.16420.20771490.18552755X-RAY DIFFRACTION98
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)
10.1580.01340.10280.30680.09410.2218-0.05740.2330.0191-0.22940.0930.0254-0.0253-0.09740.00020.2066-0.0393-0.00540.1772-0.00680.131-10.415718.4544-54.8968
20.3520.0914-0.00610.2383-0.23830.3329-0.0085-0.00120.0235-0.01390.0092-0.0114-0.03740.012-0.00010.1128-0.0122-0.00630.1212-0.00460.1152-8.763719.2957-40.4096
30.12510.0739-0.19380.2143-0.04280.2696-0.13870.0576-0.06240.34010.08830.12710.0926-0.2469-0.00050.34540.04870.03220.3073-0.02760.2031-38.89957.63-10.3903
40.1965-0.03350.00340.0834-0.02670.05750.04-0.0291-0.00340.0706-0.030.10230.05140.013-00.1277-0.0245-0.01690.1353-0.02150.1676-22.5070.4611-29.0924
50.28410.2236-0.08530.15480.00550.21550.04630.00660.14810.1610.09340.1338-0.1419-0.0330.00840.15510.02530.05640.10860.02880.1418-6.17531.063-3.2869
60.43630.2084-0.00680.4489-0.17990.14720.0624-0.0150.00970.1259-0.03180.0252-0.02390.0362-0.00010.1482-0.0097-0.00130.126-0.00890.1235-3.60074.396-20.249
70.0042-0.0027-0.00970.00330.00750.01720.0455-0.235-0.08520.13370.21920.0486-0.0167-0.0519-0.00010.2388-0.04920.03250.1756-0.00960.2038-22.1996-11.127-25.4083
80.0106-0.01350.01780.0679-0.06280.06020.02130.06670.0394-0.0386-0.00120.0824-0.07490.11790.07240.84940.23410.15860.60750.31590.5611-30.822625.4285-23.4434
90.0241-0.0209-0.00830.01810.00160.01480.00490.0591-0.1810.3449-0.02720.0862-0.22260.07680.00030.3702-0.0030.1030.19240.00640.2841-25.37259.5455-15.7761
100.043-0.0009-0.05040.0414-0.00830.05220.0460.00680.10820.2681-0.0131-0.0008-0.3136-0.1038-0.00010.30720.0277-0.02990.277-0.02960.2359-20.365312.7971-20.6937
110.093-0.0298-0.02650.01890.03620.0881-0.00890.03470.15920.09640.01220.047-0.1435-0.0833-0.00090.61310.55730.02280.31280.16150.4153-37.976420.7732-19.9443
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 5:10)
10X-RAY DIFFRACTION10(CHAIN C AND RESID 5:10)
11X-RAY DIFFRACTION11(CHAIN C AND RESID 11:14)

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