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- PDB-4b9m: Structure of the high fidelity DNA polymerase I with an oxidative... -

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Basic information

Entry
Database: PDB / ID: 4b9m
TitleStructure of the high fidelity DNA polymerase I with an oxidative formamidopyrimidine-dA DNA lesion -thymine basepair in the post- insertion site.
Components
  • 5'-D(*DC*DA*DA*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)-3'
  • DNA POLYMERASE I
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 / 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
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 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 / pdbx_struct_conn_angle / 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 / _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 / _pdbx_struct_conn_angle.value / _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 I
B: 5'-D(*GP*CP*CP*TP*GP*AP*CP*TP*CP*TP*TP)-3'
C: 5'-D(*DC*DA*DA*FAX*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
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-45.7 kcal/mol
Surface area28420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.419, 93.656, 105.053
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 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(*GP*CP*CP*TP*GP*AP*CP*TP*CP*TP*TP)-3'


Mass: 3300.159 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) GEOBACILLUS STEAROTHERMOPHILUS (bacteria)
#3: DNA chain 5'-D(*DC*DA*DA*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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Non-polymers , 3 types, 207 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.: 6 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.89 Å3/Da / Density % sol: 57.04 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 19, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 55210 / % possible obs: 99.7 % / Observed criterion σ(I): 1.5 / Redundancy: 4.1 % / Biso Wilson estimate: 24.4 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.5
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 3.9 / % possible all: 100

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Processing

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

1u45


Resolution: 2.05→50 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.939 / SU B: 9.013 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.162 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. RESIDUES 1-3 CAA IN CHAIN C ARE DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.22098 2793 5.1 %RANDOM
Rwork0.18574 ---
obs0.1875 52362 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.17 Å2
Baniso -1Baniso -2Baniso -3
1-3.2 Å20 Å20 Å2
2---1.69 Å20 Å2
3----1.51 Å2
Refinement stepCycle: LAST / Resolution: 2.05→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4653 472 31 200 5356
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0225317
X-RAY DIFFRACTIONr_bond_other_d0.0010.023527
X-RAY DIFFRACTIONr_angle_refined_deg1.5662.0917290
X-RAY DIFFRACTIONr_angle_other_deg0.94238609
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5625587
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.06224.017234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.07415883
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9541542
X-RAY DIFFRACTIONr_chiral_restr0.0940.2816
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025525
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021008
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_it0.8191.52911
X-RAY DIFFRACTIONr_mcbond_other0.2591.51164
X-RAY DIFFRACTIONr_mcangle_it1.51924699
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.6232406
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.0364.52587
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: 2.05→2.2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 207 -
Rwork0.247 3835 -
obs--99.95 %
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)
11.25320.71280.11611.53570.29070.9825-0.06730.1296-0.0701-0.18060.0634-0.02970.03040.02030.00390.0281-0.00330.00610.015-0.00470.00889.5971-18.3526-45.0139
21.1133-0.47571.1791.3377-1.43986.22270.00440.14220.03470.1105-0.079-0.05310.00460.2020.07460.12820.015-0.03170.1548-0.00020.119139.3723-8.401-9.7647
31.5403-0.0028-0.4271.29-0.06610.52470.0338-0.1580.0420.1204-0.0514-0.23080.0160.18150.01760.0519-0.00120.00220.0650.0090.055621.95130.0348-28.8554
42.29110.31651.281.73140.12451.97840.1111-0.2826-0.13510.3055-0.0356-0.150.14710.0127-0.07550.0683-0.0014-0.02050.05810.01440.03135.9804-1.6076-2.7008
50.92390.5913-0.46141.8987-0.59180.86780.0313-0.0407-0.00330.1202-0.0219-0.0601-0.04310.0145-0.00940.0081-0.0023-0.00230.0064-0.00460.00824.7371-2.8404-22.9828
65.44381.72137.81968.61822.566411.27440.32960.0882-0.0150.8046-0.2837-0.53390.4222-0.0017-0.04580.54820.0208-0.04650.5036-0.0630.400432.292-26.7414-26.6689
71.04310.31420.10270.12180.33734.15480.0399-0.0612-0.08810.045-0.0336-0.00090.1978-0.1732-0.00630.1924-0.0678-0.00990.25540.0360.23925.7469-11.321-15.3968
81.0623-0.87460.69432.2863-0.22690.54890.0406-0.08480.04880.2812-0.01880.10160.1881-0.0396-0.02180.2750.013-0.05490.2569-0.02160.199325.2102-13.8101-20.0723
97.06026.2116-0.721410.81190.71472.6888-0.15980.3804-0.94470.1560.5321-0.54631.0923-0.2384-0.37240.64270.0354-0.09260.4504-0.03130.533538.2882-29.602-21.4902
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A297 - 498
2X-RAY DIFFRACTION2A499 - 587
3X-RAY DIFFRACTION3A588 - 654
4X-RAY DIFFRACTION4A655 - 747
5X-RAY DIFFRACTION5A748 - 876
6X-RAY DIFFRACTION6B19 - 22
7X-RAY DIFFRACTION7B23 - 29
8X-RAY DIFFRACTION8C4 - 11
9X-RAY DIFFRACTION9C12 - 15

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