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- PDB-4b9v: Structure of the high fidelity DNA polymerase I with extending fr... -

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Basic information

Entry
Database: PDB / ID: 4b9v
TitleStructure of the high fidelity DNA polymerase I with extending from an oxidative formamidopyrimidine-dG DNA lesion -dA basepair.
Components
  • 5'-D(*CP*AP*TP*FOXP*AP*GP*AP*GP*TP*CP*AP*GP*GP*CP*TP)-3'
  • 5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*TP*AP*AP)-3'
  • DNA POLYMERASE
KeywordsTRANSFERASE/DNA / TRANSFERASE-DNA COMPLEX / DNA POLYMERASE / OXIDATIVE DNA LESION / DNA DAMAGE / TRANSLESION DNA SYNTHESIS
Function / homology
Function and homology information


double-strand break repair via alternative nonhomologous end joining / 3'-5' exonuclease activity / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding / metal ion binding
Similarity search - Function
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. ...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 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.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(*CP*CP*TP*GP*AP*CP*TP*CP*TP*AP*AP)-3'
C: 5'-D(*CP*AP*TP*FOXP*AP*GP*AP*GP*TP*CP*AP*GP*GP*CP*TP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,99110
Polymers78,3903
Non-polymers6017
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6240 Å2
ΔGint-111.2 kcal/mol
Surface area28130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.901, 94.035, 105.341
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 / 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(*CP*CP*TP*GP*AP*CP*TP*CP*TP*AP*AP)-3'


Mass: 3293.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: OXIDATIVE DNA LESION FAPYG AT C4 / Source: (synth.) GEOBACILLUS STEAROTHERMOPHILUS (bacteria)
#3: DNA chain 5'-D(*CP*AP*TP*FOXP*AP*GP*AP*GP*TP*CP*AP*GP*GP*CP*TP)-3'


Mass: 4650.065 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: OXIDATIVE DNA LESION FAPYG AT C4 / Source: (synth.) GEOBACILLUS STEAROTHERMOPHILUS (bacteria)

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Non-polymers , 3 types, 182 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


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


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


Mass: 18.015 Da / Num. of mol.: 175 / 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 detailsCHAIN A 1-40 DISORDERED CHAIN B RESI 1 DISORDERED CHAIN C RESIDUES 1,2 AND 15 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: 2.78 Å3/Da / Density % sol: 55.71 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.999
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 2→47 Å / Num. obs: 59511 / % possible obs: 99.8 % / Observed criterion σ(I): 1.5 / Redundancy: 5.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.9
Reflection shellResolution: 2→2.11 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 4.6 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDN ENTRY 4B9M

4b9m


Resolution: 2→47.02 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.938 / SU B: 6.15 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.149 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.21529 2965 5 %RANDOM
Rwork0.18682 ---
obs0.18824 56504 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.399 Å2
Baniso -1Baniso -2Baniso -3
1-2.12 Å20 Å20 Å2
2---1.19 Å20 Å2
3----0.93 Å2
Refinement stepCycle: LAST / Resolution: 2→47.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4648 473 31 175 5327
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0195325
X-RAY DIFFRACTIONr_bond_other_d0.0010.023562
X-RAY DIFFRACTIONr_angle_refined_deg1.5931.927307
X-RAY DIFFRACTIONr_angle_other_deg0.99538673
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5455592
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.47424.052232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.57315887
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3521541
X-RAY DIFFRACTIONr_chiral_restr0.0950.2805
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025563
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021081
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 198 -
Rwork0.211 3897 -
obs--99.59 %
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)
14.1416-2.2055-0.64063.79431.60232.2008-0.1177-0.61140.26070.38660.2588-0.1703-0.11150.0703-0.14110.13230.0063-0.01710.092-0.03720.035811.407821.103754.0956
23.4344-1.55161.13981.3028-0.0632.2787-0.0813-0.2488-0.16360.22920.08340.084-0.10050.0466-0.00210.0942-0.0241-0.00060.03480.01110.03428.661213.841846.2635
31.0103-0.9124-0.13072.21980.57661.14950.0009-0.01740.1411-0.0002-0.0014-0.0748-0.09440.03510.00040.0281-0.00610.00070.01730.00190.02349.299720.3239.7807
40.5620.5188-1.99191.171-1.44747.3412-0.0034-0.1013-0.0394-0.1615-0.0296-0.0998-0.0630.30770.0330.1758-0.03070.0140.22660.03090.162138.4617.921112.1882
52.013-0.23110.40452.46830.03580.99820.05580.1278-0.0217-0.1224-0.0624-0.2817-0.00550.1910.00650.05830.00320.00320.04140.0110.040420.3495-0.647228.2462
63.6892-0.5173-2.37731.81120.35363.20950.13320.27980.189-0.24680.0084-0.1959-0.22730.0301-0.14160.1042-0.00190.00880.05140.00510.04686.71580.93823.4508
71.45420.27271.12132.36951.78532.2737-0.01350.28740.1335-0.37160.0189-0.0989-0.20560.1402-0.00550.15160.02720.01520.08070.03260.06620.605616.3429.9735
82.1069-0.91630.77871.8341-0.84051.3020.06770.003-0.1837-0.0493-0.0280.01580.1177-0.0278-0.03970.0606-0.0062-0.01180.0075-0.00850.03797.4073-7.307329.4217
90000000000000000.129000.12900.129000
100000000000000000.129000.12900.129000
116.9751-1.5477-2.86490.35210.64121.18070.0751.2253-0.4307-0.0917-0.270.1348-0.084-0.50570.1950.74570.0292-0.20550.2509-0.03550.41117.47312.878618.5721
128.2763-1.6109-3.24030.67651.43413.050.0955-0.33530.7674-0.4423-0.0373-0.0247-0.97650.0316-0.05820.5545-0.088-0.07780.322-0.06730.261234.977820.662421.1122
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A298 - 348
2X-RAY DIFFRACTION2A349 - 408
3X-RAY DIFFRACTION3A409 - 498
4X-RAY DIFFRACTION4A499 - 597
5X-RAY DIFFRACTION5A598 - 654
6X-RAY DIFFRACTION6A655 - 734
7X-RAY DIFFRACTION7A735 - 796
8X-RAY DIFFRACTION8A797 - 876
9X-RAY DIFFRACTION9B1 - 5
10X-RAY DIFFRACTION10B6 - 11
11X-RAY DIFFRACTION11C3 - 7
12X-RAY DIFFRACTION12C8 - 14

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