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- PDB-4dfk: large fragment of DNA Polymerase I from Thermus aquaticus in a cl... -

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Basic information

Entry
Database: PDB / ID: 4dfk
Titlelarge fragment of DNA Polymerase I from Thermus aquaticus in a closed ternary complex with 5-(N-(10-hydroxydecanoyl)-aminopentinyl)-2-dUTP
Components
  • 5'-d(AAAAGGCGCCGTGGTC)-3'
  • 5'-d(GACCACGGCGC DOC)-3'
  • DNA polymerase I, thermostable
KeywordsTRANSFERASE/DNA / DNA Polymerase / TRANSFERASE-DNA complex
Function / homology
Function and homology information


nucleoside binding / 5'-3' exonuclease activity / DNA-templated DNA replication / double-strand break repair / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding
Similarity search - Function
Taq polymerase, thermostable, exonuclease region / Taq polymerase, exonuclease / 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 polymerase, thermostable, exonuclease region / Taq polymerase, exonuclease / 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 / 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 / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / 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
Chem-0L5 / FORMIC ACID / DNA / DNA (> 10) / DNA polymerase I, thermostable
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Difference Fourier Techniques / Resolution: 1.647 Å
AuthorsBergen, K. / Steck, A. / Struett, S. / Baccaro, A. / Welte, W. / Diederichs, K. / Marx, A.
CitationJournal: J.Am.Chem.Soc. / Year: 2012
Title: Structures of KlenTaq DNA Polymerase Caught While Incorporating C5-Modified Pyrimidine and C7-Modified 7-Deazapurine Nucleoside Triphosphates.
Authors: Bergen, K. / Steck, A.L. / Strutt, S. / Baccaro, A. / Welte, W. / Diederichs, K. / Marx, A.
History
DepositionJan 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2012Group: Database references
Revision 1.2Sep 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_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.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.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_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, thermostable
B: 5'-d(GACCACGGCGC DOC)-3'
C: 5'-d(AAAAGGCGCCGTGGTC)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,78418
Polymers69,5033
Non-polymers1,28215
Water6,612367
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7810 Å2
ΔGint-33 kcal/mol
Surface area24880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.211, 108.211, 90.115
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-1265-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA polymerase I, thermostable / Taq polymerase 1


Mass: 60936.965 Da / Num. of mol.: 1 / Fragment: Klenow Fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus aquaticus (bacteria) / Gene: pol I, pol1, polA / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: P19821, DNA-directed DNA polymerase

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DNA chain , 2 types, 2 molecules BC

#2: DNA chain 5'-d(GACCACGGCGC DOC)-3'


Mass: 3617.371 Da / Num. of mol.: 1 / Fragment: DNA Primer / Source method: obtained synthetically / Details: DNA synthesizer
#3: DNA chain 5'-d(AAAAGGCGCCGTGGTC)-3'


Mass: 4948.217 Da / Num. of mol.: 1 / Fragment: DNA Template / Source method: obtained synthetically / Details: DNA synthesizer

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Non-polymers , 5 types, 382 molecules

#4: Chemical ChemComp-0L5 / 2'-deoxy-5-{5-[(10-hydroxydecanoyl)amino]pent-1-yn-1-yl}uridine 5'-(tetrahydrogen triphosphate)


Mass: 719.506 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H40N3O16P3
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 367 / 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: 2.19 Å3/Da / Density % sol: 43.87 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 18% PEG 8000, 200mM Mg-Formate, 100 mMTris pH 8.0 , VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9999 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 9, 2011
RadiationMonochromator: LN2 cooled fixed-exit, Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.647→46.857 Å / Num. all: 73839 / Num. obs: 73659 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Net I/σ(I): 16.14
Reflection shellResolution: 1.65→1.75 Å / Mean I/σ(I) obs: 1.65 / Num. unique all: 11836 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.7.3_928)model building
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
XDSdata scaling
PHENIX1.7.3_928phasing
RefinementMethod to determine structure: Difference Fourier Techniques
Starting model: PDB ENTRY 3M8S

3m8s


Resolution: 1.647→46.857 Å / SU ML: 0.17 / Isotropic thermal model: isotropic and tls / Cross valid method: THROUGHOUT / σ(F): 2.01 / Phase error: 18.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1946 3699 5.02 %random
Rwork0.1703 ---
obs0.1715 73658 99.76 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.566 Å2 / ksol: 0.345 e/Å3
Displacement parametersBiso mean: 35.269 Å2
Baniso -1Baniso -2Baniso -3
1-2.3473 Å2-0 Å2-0 Å2
2--2.3473 Å2-0 Å2
3----3.454 Å2
Refinement stepCycle: LAST / Resolution: 1.647→46.857 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4260 569 79 367 5275
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095096
X-RAY DIFFRACTIONf_angle_d1.1357026
X-RAY DIFFRACTIONf_dihedral_angle_d16.6251961
X-RAY DIFFRACTIONf_chiral_restr0.07766
X-RAY DIFFRACTIONf_plane_restr0.005805
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6472-1.66890.31121240.29342537X-RAY DIFFRACTION94
1.6689-1.69170.27381320.25692690X-RAY DIFFRACTION100
1.6917-1.71590.26961410.24982650X-RAY DIFFRACTION100
1.7159-1.74150.29881430.23452689X-RAY DIFFRACTION100
1.7415-1.76870.22721490.22882649X-RAY DIFFRACTION100
1.7687-1.79770.26881320.21142687X-RAY DIFFRACTION100
1.7977-1.82870.27091500.2062666X-RAY DIFFRACTION100
1.8287-1.8620.22311520.18932651X-RAY DIFFRACTION100
1.862-1.89780.23131450.18712691X-RAY DIFFRACTION100
1.8978-1.93660.23781330.17912672X-RAY DIFFRACTION100
1.9366-1.97870.20641450.17152666X-RAY DIFFRACTION100
1.9787-2.02470.20031630.17432636X-RAY DIFFRACTION100
2.0247-2.07530.20561350.16042718X-RAY DIFFRACTION100
2.0753-2.13140.18641340.16312702X-RAY DIFFRACTION100
2.1314-2.19420.19311270.16272671X-RAY DIFFRACTION100
2.1942-2.2650.19841340.16242711X-RAY DIFFRACTION100
2.265-2.34590.19251400.16382711X-RAY DIFFRACTION100
2.3459-2.43980.22611170.17042695X-RAY DIFFRACTION100
2.4398-2.55090.18361500.17832688X-RAY DIFFRACTION100
2.5509-2.68540.23871500.17982689X-RAY DIFFRACTION100
2.6854-2.85360.21031440.18792722X-RAY DIFFRACTION100
2.8536-3.07390.22091360.18422709X-RAY DIFFRACTION100
3.0739-3.38310.19081520.17332727X-RAY DIFFRACTION100
3.3831-3.87250.15531630.14932713X-RAY DIFFRACTION100
3.8725-4.87810.15951470.13952758X-RAY DIFFRACTION100
4.8781-46.87570.18481610.16992861X-RAY DIFFRACTION100
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)
10.545-0.08720.02361.23710.19810.4571-0.0294-0.0223-0.183-0.132-0.0071-0.18550.19480.051700.2742-0.00630.02130.21460.01660.284139.8385-43.0097-17.8382
20.610.46540.02260.72850.2250.66990.0423-0.09570.08420.0083-0.03760.0334-0.12410.040100.2291-0.02560.00410.213-0.00310.237835.8576-12.6681-0.6812
30.72880.05530.04960.8089-0.36661.6505-0.0484-0.08720.04930.03340.11770.1081-0.276-0.43680.00140.23590.0376-0.00120.31530.02370.217315.2515-20.7057-11.4053
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 294:433)
2X-RAY DIFFRACTION2chain 'A' and (resseq 434:603)
3X-RAY DIFFRACTION3chain 'A' and (resseq 604:832)

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