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- PDB-4elu: Snapshot of the large fragment of DNA polymerase I from Thermus A... -

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Basic information

Entry
Database: PDB / ID: 4elu
TitleSnapshot of the large fragment of DNA polymerase I from Thermus Aquaticus processing modified pyrimidines
Components
  • DNA (5'-D(*AP*AP*AP*GP*CP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')
  • DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DDG))-3')
  • DNA polymerase I, thermostable
KeywordsTRANSFERASE/DNA / DNA polymerase / modified nucleotides / A family / DNA synthesis / rigid linker / 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-0R6 / ACETATE ION / TRIETHYLENE GLYCOL / DNA / DNA (> 10) / DNA polymerase I, thermostable
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
Synthetic DNA (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMarx, A. / Diederichs, K. / Obeid, S.
CitationJournal: Chem.Commun.(Camb.) / Year: 2012
Title: Interactions of non-polar and "Click-able" nucleotides in the confines of a DNA polymerase active site.
Authors: Obeid, S. / Busskamp, H. / Welte, W. / Diederichs, K. / Marx, A.
History
DepositionApr 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 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.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.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: DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DDG))-3')
C: DNA (5'-D(*AP*AP*AP*GP*CP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,73224
Polymers69,5193
Non-polymers2,21421
Water6,846380
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10310 Å2
ΔGint-27 kcal/mol
Surface area24330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.209, 108.209, 90.397
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-1219-

HOH

21A-1306-

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: UNP RESIDUES 293-832
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus aquaticus (bacteria) / Gene: polA, pol1 / Production host: Escherichia coli (E. coli) / References: UniProt: P19821, DNA-directed DNA polymerase

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DNA chain , 2 types, 2 molecules BC

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


Mass: 3657.395 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA primer / Source: (synth.) Synthetic DNA (others)
#3: DNA chain DNA (5'-D(*AP*AP*AP*GP*CP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')


Mass: 4924.192 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA template / Source: (synth.) Synthetic DNA (others)

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Non-polymers , 6 types, 401 molecules

#4: Chemical ChemComp-0R6 / 2'-deoxy-5-[(4-ethynylphenyl)ethynyl]cytidine 5'-(tetrahydrogen triphosphate)


Mass: 591.296 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H20N3O13P3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 380 / 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: 2.2 Å3/Da / Density % sol: 44.03 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 50 mM Na cacodylate pH=6.5, 0.2 M NH4(OAc), 10 mM Mg(OAc)2, 28% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 22, 2010
Details: Dynamically bendable mirror, LN2 cooled fixed-exit, Si(111) monochromator
RadiationMonochromator: LN2 cooled fixed-exit, Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. all: 57268 / Num. obs: 57268 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.065
Reflection shellResolution: 1.79→1.9 Å / Rmerge(I) obs: 0.724 / Mean I/σ(I) obs: 2.01 / % possible all: 97.3

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIX(phenix.refine: dev_1009)model building
PHENIX(phenix.refine: dev_1009)refinement
XDSdata reduction
PHENIXdev_1009phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3OJS

3ojs


Resolution: 1.8→46.856 Å / SU ML: 0.24 / Isotropic thermal model: isotropic and tls / Cross valid method: THROUGHOUT / σ(F): 2.01 / Phase error: 17.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1825 2857 5.02 %Random
Rwork0.1553 ---
obs0.1567 56899 99.98 %-
all-56899 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.8621 Å2-0 Å20 Å2
2--6.8621 Å20 Å2
3---3.9249 Å2
Refinement stepCycle: LAST / Resolution: 1.8→46.856 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4286 570 131 380 5367
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065185
X-RAY DIFFRACTIONf_angle_d1.1887123
X-RAY DIFFRACTIONf_dihedral_angle_d16.4312023
X-RAY DIFFRACTIONf_chiral_restr0.075770
X-RAY DIFFRACTIONf_plane_restr0.005824
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.83110.28871410.23252696X-RAY DIFFRACTION100
1.8311-1.86440.2611430.21362650X-RAY DIFFRACTION100
1.8644-1.90020.26111320.2052665X-RAY DIFFRACTION100
1.9002-1.9390.23011340.18912685X-RAY DIFFRACTION100
1.939-1.98120.23161560.17322668X-RAY DIFFRACTION100
1.9812-2.02730.22931390.17232669X-RAY DIFFRACTION100
2.0273-2.0780.22771670.16562679X-RAY DIFFRACTION100
2.078-2.13420.20841220.16042700X-RAY DIFFRACTION100
2.1342-2.1970.2011320.15282679X-RAY DIFFRACTION100
2.197-2.26790.18921310.1492718X-RAY DIFFRACTION100
2.2679-2.34890.21831400.1552686X-RAY DIFFRACTION100
2.3489-2.4430.20181190.1612706X-RAY DIFFRACTION100
2.443-2.55410.19941470.1622677X-RAY DIFFRACTION100
2.5541-2.68880.20141510.16062684X-RAY DIFFRACTION100
2.6888-2.85720.19981440.16242721X-RAY DIFFRACTION100
2.8572-3.07780.18881370.15752718X-RAY DIFFRACTION100
3.0778-3.38740.16251510.15042714X-RAY DIFFRACTION100
3.3874-3.87740.15991640.13672711X-RAY DIFFRACTION100
3.8774-4.88430.15031460.13152763X-RAY DIFFRACTION100
4.8843-46.87170.16741610.16732853X-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)
11.8610.1326-0.05232.73090.13741.558-0.09360.0752-0.2878-0.3285-0.0091-0.34480.29560.09270.08690.2853-0.00020.0670.1595-0.00910.233539.392-42.9628-18.0504
21.09790.69680.1091.52730.84872.33890.0358-0.21260.12180.0065-0.06290.0596-0.22290.08920.02430.12380.0142-0.01350.16240.01560.175536.8001-11.04792.7472
31.33290.1334-0.40550.72540.06661.3288-0.02280.00990.0484-0.0663-0.00560.0982-0.1051-0.23290.01760.1983-0.0007-0.03680.2109-0.00730.177317.8568-19.9432-11.516
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 294:433)
2X-RAY DIFFRACTION2chain 'A' and (resseq 434:562)
3X-RAY DIFFRACTION3chain 'A' and (resseq 563:832)

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