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- PDB-4b9t: Structure of the high fidelity DNA polymerase I with an oxidative... -

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Basic information

Entry
Database: PDB / ID: 4b9t
TitleStructure of the high fidelity DNA polymerase I with an oxidative formamidopyrimidine-dG DNA lesion -dC basepair in the post-insertion site.
Components
  • 5'-D(*AP*CP*CP*TP*GP*AP*CP*TP*CP*TP)-3'
  • 5'-D(*CP*AP*TP*FOXP*AP*GP*AP*GP*TP*CP*AP*GP*GP*TP*TP)-3'
  • DNA POLYMERASE
KeywordsTRANSFERASE/DNA / TRANSFERASE-DNA COMPLEX / OXIDATIVE DNA LESION / DNA DAMAGE / TRANSLESION DNA 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 / 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
DNA / DNA (> 10) / DNA polymerase I
Similarity search - Component
Biological speciesGEOBACILLUS STEAROTHERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 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 6, 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 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_conn_type.id / _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
B: 5'-D(*AP*CP*CP*TP*GP*AP*CP*TP*CP*TP)-3'
C: 5'-D(*CP*AP*TP*FOXP*AP*GP*AP*GP*TP*CP*AP*GP*GP*TP*TP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,6176
Polymers78,4013
Non-polymers2163
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4870 Å2
ΔGint-42.2 kcal/mol
Surface area28380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.381, 93.775, 105.608
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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Protein , 1 types, 1 molecules A

#1: Protein DNA POLYMERASE / 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

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DNA chain , 2 types, 2 molecules BC

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


Mass: 3310.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) GEOBACILLUS STEAROTHERMOPHILUS (bacteria)
#3: DNA chain 5'-D(*CP*AP*TP*FOXP*AP*GP*AP*GP*TP*CP*AP*GP*GP*TP*TP)-3'


Mass: 4644.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) GEOBACILLUS STEAROTHERMOPHILUS (bacteria)

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Non-polymers , 3 types, 62 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer details((1R,2S,4R)-4-{[2-AMINO-5-(FORMYLAMINO)-6-OXO-3, 6-DIHYDROPYRIMIDIN-4-YL]AMINO}-2- ...((1R,2S,4R)-4-{[2-AMINO-5-(FORMYLAMINO)-6-OXO-3, 6-DIHYDROPYRIMIDIN-4-YL]AMINO}-2-HYDROXYCYCLOPENTYL)METHYL 5'-PHOSPHATE (FOX): ALSO PRESENT IN PDB CODE 1TDZ
Sequence details1-39 DISORDERED RESIDUES 1-3 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: 3.01 Å3/Da / Density % sol: 58.75 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 28, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.65→43.3 Å / Num. obs: 24741 / % possible obs: 97.1 % / Observed criterion σ(I): 1.5 / Redundancy: 5.9 % / Biso Wilson estimate: 46.2 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 17.6
Reflection shellResolution: 2.65→2.79 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 4 / % possible all: 97.1

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Processing

Software
NameVersionClassification
REFMAC5.5.0110refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1U45

1u45


Resolution: 2.65→45 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.868 / SU B: 27.055 / SU ML: 0.256 / Cross valid method: THROUGHOUT / ESU R: 0.856 / ESU R Free: 0.353 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27302 1240 5 %RANDOM
Rwork0.22138 ---
obs0.22395 23432 94.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.531 Å2
Baniso -1Baniso -2Baniso -3
1-4.77 Å20 Å20 Å2
2---2.37 Å20 Å2
3----2.4 Å2
Refinement stepCycle: LAST / Resolution: 2.65→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4653 473 11 59 5196
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225278
X-RAY DIFFRACTIONr_bond_other_d00.023496
X-RAY DIFFRACTIONr_angle_refined_deg1.1812.097232
X-RAY DIFFRACTIONr_angle_other_deg4.0138536
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6615581
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.80124.138232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.83915874
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0691540
X-RAY DIFFRACTIONr_chiral_restr0.0670.2812
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215494
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02998
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9641.52902
X-RAY DIFFRACTIONr_mcbond_other01.51161
X-RAY DIFFRACTIONr_mcangle_it1.70624680
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9332376
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5564.52551
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.65→2.8 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 91 -
Rwork0.306 1733 -
obs--96.76 %
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)
10.36820.16430.0940.2345-0.08650.3381-0.03050.0351-0.0085-0.02640.0286-0.02270.01320.01410.00190.5506-0.002-0.00830.52990.00240.5296-9.925516.8482-50.3758
20.9409-0.03260.33550.499-0.08560.7343-0.0109-0.06970.04090.00190.02060.0352-0.0396-0.051-0.00980.53840.0016-0.00350.51030.00830.5326-13.335228.5946-42.38
30.21420.15460.00240.2609-0.00160.10120.0109-0.0088-0.048-0.0196-0.0218-0.06970.01970.02420.01090.54820.0004-0.00440.53740.00220.5366-8.39957.981-35.0804
40.351-0.4485-0.27551.45550.51822.844-0.01520.28280.01480.05710.0268-0.0776-0.06170.0576-0.01160.48110.01520.03050.45310.02310.4265-40.528410.6737-6.8147
50.2908-0.1206-0.1610.060.06530.09-0.0109-0.0466-0.0613-0.0073-0.0322-0.0267-0.01260.03380.04310.5610.0001-0.00350.56130.00180.5477-26.01793.322-25.1803
60.42520.04150.42350.04560.0810.4651-0.02760.02370.0062-0.00750.01470.01680.02050.04230.01290.54620.0005-0.0010.52810.00450.5261-5.8097-5.2936-18.3171
70.85310.0242-0.24031.4889-0.16210.79250.0366-0.01890.09720.0216-0.04540.0983-0.09250.05660.00880.5365-0.00140.03070.5097-0.01340.5088-9.6753.1860.6753
80.11360.16450.11230.26320.16060.11160.0137-0.0014-0.00230.01970.0004-0.00050.005-0.0027-0.01410.5531-0.0021-0.00520.53420.00180.545-4.54883.0664-22.5159
98.56337.2342-4.26696.6242-3.49052.15240.6453-0.16180.26140.4767-0.42380.1459-0.39790.032-0.22150.51920.048-0.0140.30010.09480.3745-31.54526.0004-24.401
100.11490.0704-0.56750.0456-0.33772.8496-0.053-0.0568-0.05650.0486-0.1308-0.0246-0.01730.18360.18380.5287-0.0092-0.02390.57320.04120.5095-24.90899.2812-15.3636
111.77120.6262-2.00151.3490.8364.3832-0.14040.4084-0.18460.02870.2071-0.22370.0807-0.1977-0.06660.47520.1215-0.13920.3510.14250.4232-25.149413.9349-20.1252
1218.63310.6434-13.626.685-7.307710.32641.7498-1.11432.55820.7934-0.64122.3563-1.33460.7896-1.10860.86730.30240.09030.2975-0.17621.6947-37.97729.8349-21.5093
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A297 - 404
2X-RAY DIFFRACTION2A405 - 458
3X-RAY DIFFRACTION3A459 - 503
4X-RAY DIFFRACTION4A504 - 572
5X-RAY DIFFRACTION5A573 - 638
6X-RAY DIFFRACTION6A639 - 681
7X-RAY DIFFRACTION7A682 - 743
8X-RAY DIFFRACTION8A744 - 876
9X-RAY DIFFRACTION9B19 - 23
10X-RAY DIFFRACTION10B24 - 29
11X-RAY DIFFRACTION11C4 - 11
12X-RAY DIFFRACTION12C12 - 15

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