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

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Basic information

Entry
Database: PDB / ID: 3tan
TitleCrystal Structure of Bacillus DNA Polymerase I Large Fragment Bound to Duplex DNA with Cytosine-Adenine Mismatch at (n-1) Position
Components
  • 5'-D(*GP*AP*CP*GP*T*AP*CP*GP*TP*GP*AP*TP*CP*GP*CP*A)-3'
  • 5'-D(*GP*CP*GP*AP*TP*CP*AP*CP*GP*C)-3'
  • DNA polymerase I
KeywordsTRANSFERASE/DNA / DNA Polymerase I / protein-DNA complex / TRANSFERASE-DNA complex
Function / homology
Function and homology information


Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / Alpha-Beta Plaits - #370 / 5' to 3' exonuclease, C-terminal subdomain / Ribonuclease H-like superfamily/Ribonuclease H / DNA polymerase; domain 1 / Nucleotidyltransferase; domain 5 / Alpha-Beta Plaits / Up-down Bundle / 2-Layer Sandwich ...Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / Alpha-Beta Plaits - #370 / 5' to 3' exonuclease, C-terminal subdomain / Ribonuclease H-like superfamily/Ribonuclease H / DNA polymerase; domain 1 / Nucleotidyltransferase; domain 5 / Alpha-Beta Plaits / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
sucrose / 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / :
Similarity search - Component
Biological speciesGeobacillus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.53 Å
AuthorsWang, W. / Beese, L.S.
Citation
Journal: 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.
#1: Journal: Cell(Cambridge,Mass.) / Year: 2004
Title: Structures of mismatch replication errors observed in a DNA polymerase.
Authors: Johnson, S.J. / Beese, L.S.
History
DepositionAug 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2011Group: Database references
Revision 1.2Apr 2, 2014Group: Source and taxonomy
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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*GP*AP*TP*CP*AP*CP*GP*C)-3'
C: 5'-D(*GP*AP*CP*GP*T*AP*CP*GP*TP*GP*AP*TP*CP*GP*CP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,6659
Polymers75,4713
Non-polymers1,1946
Water15,727873
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5780 Å2
ΔGint-51 kcal/mol
Surface area27950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.430, 93.010, 105.330
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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DNA chain , 2 types, 2 molecules BC

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


Mass: 3029.994 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Primer Strand
#3: DNA chain 5'-D(*GP*AP*CP*GP*T*AP*CP*GP*TP*GP*AP*TP*CP*GP*CP*A)-3'


Mass: 4923.204 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Template Strand

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein DNA polymerase I


Mass: 67518.297 Da / Num. of mol.: 1 / Fragment: Bacillus Fragment (UNP residues 285-876)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus (bacteria) / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: C9RTX7, DNA-directed DNA polymerase
#4: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 3 types, 878 molecules

#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-DCP / 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O13P3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 873 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE AUTHORS STATE THAT THE GEOBACILLUS SP. STRAIN IS UNKNOWN BUT SIMILAR TO Y412MC61.

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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: 2.84 Å3/Da / Density % sol: 56.65 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 45-50% saturated ammonium sulfate, 2.5% MPD, 10 mM magnesium sulfate, 100 mM MES, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.111 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 27, 2009
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.111 Å / Relative weight: 1
ReflectionResolution: 1.53→50 Å / Num. obs: 127023 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.033 / Net I/σ(I): 26.2
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.53-1.620.484.1199.6
1.62-1.730.2766.71199.4
1.73-1.870.15810.99198.7
1.87-2.050.08119.1198
2.05-2.290.04431.07197.6
2.29-2.650.03140.52198.1
2.65-3.240.02252.09198.3
3.24-4.560.01576.09196.3
4.56-500.01577.9185.5

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1L3T

1l3t


Resolution: 1.53→41.058 Å / Occupancy max: 1 / Occupancy min: 0.27 / SU ML: 0.28 / σ(F): 2.35 / Phase error: 18.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1845 5577 4.61 %
Rwork0.1696 --
obs0.1704 120984 93.28 %
Solvent computationShrinkage radii: 0.65 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.363 Å2 / ksol: 0.474 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.1293 Å2-0 Å2-0 Å2
2---3.274 Å20 Å2
3----2.8554 Å2
Refinement stepCycle: LAST / Resolution: 1.53→41.058 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4654 424 63 873 6014
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115299
X-RAY DIFFRACTIONf_angle_d1.3587263
X-RAY DIFFRACTIONf_dihedral_angle_d15.4612029
X-RAY DIFFRACTIONf_chiral_restr0.073819
X-RAY DIFFRACTIONf_plane_restr0.007861
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.53-1.54740.25531820.22583461X-RAY DIFFRACTION85
1.5474-1.56560.24281860.21213522X-RAY DIFFRACTION88
1.5656-1.58470.22251880.20253578X-RAY DIFFRACTION88
1.5847-1.60480.24211900.20043618X-RAY DIFFRACTION89
1.6048-1.62590.21551910.19533621X-RAY DIFFRACTION89
1.6259-1.64810.20781920.18513653X-RAY DIFFRACTION90
1.6481-1.67170.21751980.18443751X-RAY DIFFRACTION91
1.6717-1.69660.19231620.17663710X-RAY DIFFRACTION91
1.6966-1.72320.17251020.16883877X-RAY DIFFRACTION92
1.7232-1.75140.20171250.17483839X-RAY DIFFRACTION93
1.7514-1.78160.19811190.17423863X-RAY DIFFRACTION93
1.7816-1.8140.17721620.16823784X-RAY DIFFRACTION93
1.814-1.84890.19531690.17483890X-RAY DIFFRACTION94
1.8489-1.88660.18061480.17483860X-RAY DIFFRACTION94
1.8866-1.92770.19491730.17483881X-RAY DIFFRACTION94
1.9277-1.97250.18551630.16623937X-RAY DIFFRACTION95
1.9725-2.02180.17631970.16943957X-RAY DIFFRACTION96
2.0218-2.07650.16251780.16483942X-RAY DIFFRACTION96
2.0765-2.13760.17081890.15713930X-RAY DIFFRACTION96
2.1376-2.20660.19931980.15463946X-RAY DIFFRACTION96
2.2066-2.28540.17692270.14563929X-RAY DIFFRACTION96
2.2854-2.37690.15192130.15863943X-RAY DIFFRACTION96
2.3769-2.48510.14831980.15994010X-RAY DIFFRACTION97
2.4851-2.61610.1832380.1643992X-RAY DIFFRACTION97
2.6161-2.780.1742260.17074011X-RAY DIFFRACTION97
2.78-2.99460.1992110.17854071X-RAY DIFFRACTION98
2.9946-3.29580.19192230.1724058X-RAY DIFFRACTION98
3.2958-3.77240.19862090.16014091X-RAY DIFFRACTION97
3.7724-4.75170.15682210.15143950X-RAY DIFFRACTION94
4.7517-41.07280.20061990.19983732X-RAY DIFFRACTION85

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