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

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Basic information

Entry
Database: PDB / ID: 3tap
TitleCrystal Structure of Bacillus DNA Polymerase I Large Fragment Bound to Duplex DNA with Cytosine-Adenine Mismatch at (n-3) Position
Components
  • 5'-D(*G*CP*GP*AP*TP*CP*AP*CP*GP*CP*AP*C)-3'
  • 5'-D(*GP*A*CP*GP*TP*AP*CP*GP*TP*GP*AP*TP*CP*GP*CP*A)-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 / DNA / DNA (> 10) / :
Similarity search - Component
Biological speciesGeobacillus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.655 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 / database_PDB_caveat / 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_struct_conn_angle / pdbx_validate_chiral / 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_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_label_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 / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_atom_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.auth_seq_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(*G*CP*GP*AP*TP*CP*AP*CP*GP*CP*AP*C)-3'
C: 5'-D(*GP*A*CP*GP*TP*AP*CP*GP*TP*GP*AP*TP*CP*GP*CP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,0719
Polymers76,0743
Non-polymers9976
Water12,556697
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6150 Å2
ΔGint-53 kcal/mol
Surface area28150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.660, 93.270, 105.700
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(*G*CP*GP*AP*TP*CP*AP*CP*GP*CP*AP*C)-3'


Mass: 3632.382 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Primer Strand
#3: DNA chain 5'-D(*GP*A*CP*GP*TP*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, 3 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.: 2
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, 701 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 697 / 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: 56.69 %
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: APS / Beamline: 22-BM / Wavelength: 0.97121 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 23, 2009
RadiationMonochromator: Rosenbaum-Rock double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97121 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 102589 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.045 / Net I/σ(I): 19.92
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.65-1.760.4893.43191.6
1.76-1.880.2885.7199.9
1.88-2.030.1579.73199.8
2.03-2.220.08716.27199.6
2.22-2.480.05922.35199.2
2.48-2.860.04428.61199.2
2.86-3.510.0338.98199.1
3.51-4.950.02351.37199.3
4.95-500.01860.76197.9

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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 1L5U

1l5u


Resolution: 1.655→40.719 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.32 / σ(F): 2.35 / Phase error: 19.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.202 4724 4.88 %
Rwork0.176 --
obs0.1773 96815 93.42 %
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.157 Å2 / ksol: 0.446 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.4319 Å2-0 Å2-0 Å2
2---3.3351 Å20 Å2
3----4.0968 Å2
Refinement stepCycle: LAST / Resolution: 1.655→40.719 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4650 463 62 697 5872
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095339
X-RAY DIFFRACTIONf_angle_d1.2237327
X-RAY DIFFRACTIONf_dihedral_angle_d15.8472042
X-RAY DIFFRACTIONf_chiral_restr0.113834
X-RAY DIFFRACTIONf_plane_restr0.006862
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6551-1.67390.30041170.26852218X-RAY DIFFRACTION69
1.6739-1.69360.29841460.24112768X-RAY DIFFRACTION85
1.6936-1.71430.24251460.22972766X-RAY DIFFRACTION86
1.7143-1.7360.27781460.21452775X-RAY DIFFRACTION86
1.736-1.75880.21141520.21182889X-RAY DIFFRACTION88
1.7588-1.78290.27181500.20642866X-RAY DIFFRACTION89
1.7829-1.80840.26511520.20082884X-RAY DIFFRACTION89
1.8084-1.83540.21541560.19782958X-RAY DIFFRACTION90
1.8354-1.86410.21671540.18882931X-RAY DIFFRACTION90
1.8641-1.89460.22011560.18382962X-RAY DIFFRACTION92
1.8946-1.92730.21561580.18162994X-RAY DIFFRACTION92
1.9273-1.96230.22241440.183091X-RAY DIFFRACTION94
1.9623-2.00010.19851170.17863144X-RAY DIFFRACTION95
2.0001-2.04090.19271420.17183151X-RAY DIFFRACTION96
2.0409-2.08530.18191470.16573131X-RAY DIFFRACTION96
2.0853-2.13380.18641620.16233145X-RAY DIFFRACTION96
2.1338-2.18710.18521580.16683162X-RAY DIFFRACTION97
2.1871-2.24630.19051660.16453156X-RAY DIFFRACTION96
2.2463-2.31240.18951800.15593129X-RAY DIFFRACTION97
2.3124-2.3870.20131740.16593183X-RAY DIFFRACTION97
2.387-2.47230.18681740.16163191X-RAY DIFFRACTION97
2.4723-2.57130.21751730.16043187X-RAY DIFFRACTION97
2.5713-2.68830.16471590.17443230X-RAY DIFFRACTION98
2.6883-2.830.22451790.17353222X-RAY DIFFRACTION98
2.83-3.00720.19591590.17853265X-RAY DIFFRACTION98
3.0072-3.23930.20051480.17853282X-RAY DIFFRACTION99
3.2393-3.56510.20381840.16473262X-RAY DIFFRACTION98
3.5651-4.08060.17771680.15583329X-RAY DIFFRACTION99
4.0806-5.13950.16731610.16233383X-RAY DIFFRACTION99
5.1395-40.73170.2271960.20943437X-RAY DIFFRACTION98

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