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- PDB-4b9u: Structure of the high fidelity DNA polymerase I with an oxidative... -

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Basic information

Entry
Database: PDB / ID: 4b9u
TitleStructure of the high fidelity DNA polymerase I with an oxidative formamidopyrimidine-dG DNA lesion -dA basepair in the post-insertion site.
Components
  • 5'-D(*CP*AP*AP*FOXP*CP*GP*AP*GP*TP*CP*AP*GP*GP*CP*TP)-3'
  • 5'-D(*GP*CP*CP*TP*GP*AP*CP*TP*CP*GP*AP)-3'
  • DNA POLYMERASE
KeywordsTRANSFERASE/DNA / TRANSFERASE-DNA COMPLEX / OXIDATIVE DNA LESION / DNA DAMAGE / TRANSLESION DNA 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 / 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: 2.1 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(*GP*CP*CP*TP*GP*AP*CP*TP*CP*GP*AP)-3'
C: 5'-D(*CP*AP*AP*FOXP*CP*GP*AP*GP*TP*CP*AP*GP*GP*CP*TP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,9209
Polymers78,4163
Non-polymers5056
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6190 Å2
ΔGint-84.6 kcal/mol
Surface area28400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.748, 93.853, 105.648
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(*GP*CP*CP*TP*GP*AP*CP*TP*CP*GP*AP)-3'


Mass: 3334.186 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*AP*FOXP*CP*GP*AP*GP*TP*CP*AP*GP*GP*CP*TP)-3'


Mass: 4635.054 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, 197 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / 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.: 191 / 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 AND 2 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: 56.33 % / 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: Aug 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→46.3 Å / Num. obs: 51802 / % possible obs: 99 % / Observed criterion σ(I): 1.5 / Redundancy: 4.5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.6
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 3.3 / % possible all: 99.3

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Processing

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

4b9m


Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.933 / SU B: 8.42 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22356 2590 5 %RANDOM
Rwork0.19143 ---
obs0.19305 49156 99.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.63 Å2
Baniso -1Baniso -2Baniso -3
1-2.97 Å20 Å20 Å2
2---1.94 Å20 Å2
3----1.03 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4653 495 26 191 5365
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0195315
X-RAY DIFFRACTIONr_bond_other_d0.0010.023547
X-RAY DIFFRACTIONr_angle_refined_deg1.5761.9157289
X-RAY DIFFRACTIONr_angle_other_deg0.99838626
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7825581
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.91424.113231
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.61215875
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6371540
X-RAY DIFFRACTIONr_chiral_restr0.0890.2799
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025539
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021082
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: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 181 -
Rwork0.268 3348 -
obs--98.66 %
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)
12.16550.80510.22352.01350.77651.5037-0.08950.4658-0.1-0.23360.1483-0.02570.05210.056-0.05880.1084-0.00610.03350.1034-0.01540.032311.3489-21.0094-54.22
21.8840.5181-0.59071.0502-0.06491.2381-0.03570.14210.125-0.1570.0290.07670.06010.01450.00680.04510.0010.00160.01460.01270.04578.6727-13.7256-46.3523
30.90010.58150.07151.31240.32560.7311-0.01530.0216-0.0792-0.0310.0105-0.02730.07510.01190.00480.0270.00510.00580.00680.00550.01669.3201-20.2029-39.8876
40.37-0.06911.17060.5706-0.43483.83050.01650.06710.04420.062-0.1053-0.0560.07090.2160.08880.15770.0254-0.02610.21280.02780.146738.6759-7.9651-12.2425
51.12810.1386-0.21911.56540.09950.52130.0293-0.12440.03170.1259-0.01-0.20660.06310.1329-0.01930.0640.0066-0.00620.05050.00630.062420.4730.6816-28.3948
61.8560.00420.88561.11030.13341.550.0845-0.1911-0.10090.14920.009-0.1180.0740.02-0.09350.0672-0.01-0.01490.03170.00990.04646.981-0.8911-3.4704
71.02450.1589-0.26521.80341.05430.8860.0471-0.1524-0.11440.314-0.0587-0.10660.18030.05090.01150.1127-0.0194-0.01570.03290.03170.05030.6642-16.2659-9.9983
81.32160.4478-0.61831.1955-0.65281.2320.04730.02630.0840.0329-0.0008-0.0199-0.08890.0021-0.04650.04420.00360.0130.0064-0.01150.0487.5557.3733-29.5074
91.71352.24034.49654.79155.477812.00220.2169-0.0257-0.05540.2902-0.07170.04550.5328-0.2268-0.14530.19740.04130.01430.2475-0.06880.15131.8019-25.7744-24.5289
100.44840.2973-0.03050.20040.03381.23190.1252-0.03620.12920.1087-0.05420.08420.0361-0.0929-0.07110.1182-0.0130.03110.0528-0.02410.068524.5839-9.1756-15.6009
113.46511.9514-2.96632.0416-1.50615.8041-0.1393-0.4241-0.05750.3608-0.19320.02640.3640.13980.33260.30890.01180.0160.22160.03070.205617.6257-14.5084-15.3707
124.4876-0.08230.60020.96140.94031.03070.07540.0132-0.3720.27880.0062-0.00270.3160.0349-0.08160.25490.0443-0.00780.1981-0.02590.184135.1899-20.6726-21.1947
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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