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- PDB-3px6: Crystal Structure of Bacillus DNA Polymerase I Large Fragment Bou... -

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Basic information

Entry
Database: PDB / ID: 3px6
TitleCrystal Structure of Bacillus DNA Polymerase I Large Fragment Bound to DNA and ddCTP-dA Mismatch (tautomer) in Closed Conformation
Components
  • DNA (5'-D(*C*AP*TP*AP*GP*GP*AP*GP*TP*CP*AP*GP*G)-3')
  • DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DOC))-3')
  • DNA polymerase I
KeywordsTRANSFERASE/DNA / DNA Polymerase I / protein-DNA complex / TRANSFERASE-DNA complex / Cytosine-Adenine / closed conformation
Function / homology
Function and homology information


5'-3' exonuclease activity / 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 I-like, H3TH domain / 5'-3' exonuclease, C-terminal SAM fold / 5'-3' exonuclease, alpha-helical arch, N-terminal / 5'-3' exonuclease, N-terminal resolvase-like domain / 5'-3' exonuclease / 5'-3' exonuclease / DNA polymerase 1 / Taq DNA Polymerase; Chain T, domain 4 ...: / DNA polymerase I, ribonuclease H-like domain / DNA polymerase I-like, H3TH domain / 5'-3' exonuclease, C-terminal SAM fold / 5'-3' exonuclease, alpha-helical arch, N-terminal / 5'-3' exonuclease, N-terminal resolvase-like domain / 5'-3' exonuclease / 5'-3' exonuclease / DNA polymerase 1 / Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / Alpha-Beta Plaits - #370 / Helix-hairpin-helix motif, class 2 / Helix-hairpin-helix class 2 (Pol1 family) motifs / 5'-3' exonuclease, C-terminal domain superfamily / 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 / PIN-like domain superfamily / 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
2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE / : / DNA / DNA (> 10) / DNA polymerase I
Similarity search - Component
Biological speciesGeobacillus kaustophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.59 Å
AuthorsWang, W. / Beese, L.S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis.
Authors: Wang, W. / Hellinga, H.W. / Beese, L.S.
History
DepositionDec 9, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2011Group: Database references
Revision 1.2Nov 9, 2011Group: Database references
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details / _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
D: DNA polymerase I
B: DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DOC))-3')
C: DNA (5'-D(*C*AP*TP*AP*GP*GP*AP*GP*TP*CP*AP*GP*G)-3')
E: DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DOC))-3')
F: DNA (5'-D(*C*AP*TP*AP*GP*GP*AP*GP*TP*CP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,18115
Polymers148,3336
Non-polymers1,8489
Water21,6541202
1
A: DNA polymerase I
B: DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DOC))-3')
C: DNA (5'-D(*C*AP*TP*AP*GP*GP*AP*GP*TP*CP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,3168
Polymers74,1673
Non-polymers1,1495
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6350 Å2
ΔGint-30 kcal/mol
Surface area27660 Å2
MethodPISA
2
D: DNA polymerase I
E: DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DOC))-3')
F: DNA (5'-D(*C*AP*TP*AP*GP*GP*AP*GP*TP*CP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,8657
Polymers74,1673
Non-polymers6984
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6650 Å2
ΔGint-56 kcal/mol
Surface area27860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.460, 108.280, 149.760
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, 2 molecules AD

#1: Protein DNA polymerase I


Mass: 67490.289 Da / Num. of mol.: 2
Fragment: Bacillus Fragment (analogous to E. coli Klenow Fragment)
Mutation: D598A, F710Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus kaustophilus (bacteria) / Gene: polA, GK2730 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q5KWC1, DNA-directed DNA polymerase

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DNA chain , 2 types, 4 molecules BECF

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


Mass: 2635.751 Da / Num. of mol.: 2 / Fragment: DNA primer strand / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*C*AP*TP*AP*GP*GP*AP*GP*TP*CP*AP*GP*G)-3')


Mass: 4040.647 Da / Num. of mol.: 2 / Fragment: DNA template strand / Source method: obtained synthetically

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Non-polymers , 4 types, 1211 molecules

#4: Chemical ChemComp-DCT / 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE


Type: DNA linking / Mass: 451.158 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H16N3O12P3
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#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.: 1202 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsAUTHORS STATE THAT THE PROTEIN WAS ISOLATED FROM A STRAIN OF GEOBACILLUS SPECIES WHOSE SEQUENCE IS ...AUTHORS STATE THAT THE PROTEIN WAS ISOLATED FROM A STRAIN OF GEOBACILLUS SPECIES WHOSE SEQUENCE IS NOT AVAILABLE IN THE UNIPROT DATABASE. IT DIFFERS FROM UNP Q5KWC1 BY THIS SINGLE RESIDUE.

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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: 2.55 Å3/Da / Density % sol: 51.85 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: Ammonium Sulfate, MPD, MgSO4, MnSO4, MES, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Components of the solutions
IDNameCrystal-IDSol-ID
1Ammonium Sulfate11
2MPD11
3MgSO411
4MnSO411
5MES11
6Ammonium Sulfate12
7MPD12
8MgSO412
9MnSO412
10MES12

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.1158 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionResolution: 1.59→100 Å / Num. all: 203609 / Num. obs: 201565 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 8.3 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 17.61
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.59-1.680.5643.2199.9
1.68-1.80.3045.71100
1.8-1.950.1778.9196.2
1.95-2.130.23215.91100
2.13-2.380.16121196.9
2.38-2.750.09129.31100
2.75-3.370.06234.81100
3.37-4.760.04938.9199.6
4.76-1000.04440199.2

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.1_743refinement
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 2HVI with insertion site base pair, metal ions, and protein residues 680-717 deleted

2hvi


Resolution: 1.59→87.747 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.948 / Occupancy max: 1 / Occupancy min: 0.39 / SU ML: 0.39 / σ(F): 2.35 / Phase error: 19.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2071 8800 4.57 %
Rwork0.1846 --
obs0.1857 192561 94.58 %
all-203609 -
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.581 Å2 / ksol: 0.402 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.0381 Å2-0 Å2-0 Å2
2---0.8928 Å20 Å2
3----1.1453 Å2
Refinement stepCycle: LAST / Resolution: 1.59→87.747 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9302 848 103 1202 11455
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01310622
X-RAY DIFFRACTIONf_angle_d1.48914575
X-RAY DIFFRACTIONf_dihedral_angle_d17.1954119
X-RAY DIFFRACTIONf_chiral_restr0.0821624
X-RAY DIFFRACTIONf_plane_restr0.0081737
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.59-1.60810.27592870.255453X-RAY DIFFRACTION85
1.6081-1.6270.25282960.23715626X-RAY DIFFRACTION89
1.627-1.64680.24562990.22135672X-RAY DIFFRACTION89
1.6468-1.66770.28443030.23155748X-RAY DIFFRACTION90
1.6677-1.68960.25563030.21645772X-RAY DIFFRACTION91
1.6896-1.71280.2543100.21155893X-RAY DIFFRACTION92
1.7128-1.73730.24843150.20165975X-RAY DIFFRACTION93
1.7373-1.76320.23823150.19825984X-RAY DIFFRACTION93
1.7632-1.79070.25563170.1996017X-RAY DIFFRACTION94
1.7907-1.82010.22153190.18986070X-RAY DIFFRACTION95
1.8201-1.85150.23473220.18696118X-RAY DIFFRACTION96
1.8515-1.88520.22513210.18396092X-RAY DIFFRACTION95
1.8852-1.92140.40362690.31465111X-RAY DIFFRACTION80
1.9214-1.96070.28672800.24675330X-RAY DIFFRACTION83
1.9607-2.00330.23272560.18566298X-RAY DIFFRACTION97
2.0033-2.04990.17912230.17346452X-RAY DIFFRACTION98
2.0499-2.10120.1832520.16666428X-RAY DIFFRACTION99
2.1012-2.1580.18592600.16756423X-RAY DIFFRACTION99
2.158-2.22150.19842970.17496284X-RAY DIFFRACTION97
2.2215-2.29320.2852070.24325570X-RAY DIFFRACTION85
2.2932-2.37520.19442660.15996459X-RAY DIFFRACTION99
2.3752-2.47030.18392600.16256513X-RAY DIFFRACTION99
2.4703-2.58270.19452720.1736499X-RAY DIFFRACTION100
2.5827-2.71890.18942780.17496521X-RAY DIFFRACTION100
2.7189-2.88920.21222990.17476505X-RAY DIFFRACTION100
2.8892-3.11230.19853160.18286519X-RAY DIFFRACTION100
3.1123-3.42550.17783370.17046514X-RAY DIFFRACTION100
3.4255-3.92120.17453310.16466519X-RAY DIFFRACTION99
3.9212-4.94030.17463420.15676601X-RAY DIFFRACTION100
4.9403-87.88080.21843480.21116795X-RAY DIFFRACTION99

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