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- PDB-3m8r: Crystal structure of the large fragment of DNA polymerase I from ... -

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Basic information

Entry
Database: PDB / ID: 3m8r
TitleCrystal structure of the large fragment of DNA polymerase I from Thermus aquaticus in a closed ternary complex with trapped 4'-ethylated dTTP
Components
  • DNA (5'-D(*AP*AP*AP*AP*GP*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*(DOC))-3')
  • DNA polymerase I, thermostable
KeywordsTransferase/DNA / DNA / DNA polymerase / DNA replication / nucleotides / modified nucleotide / artificial nucleotide / nucleotide probes / DNA-binding / DNA-directed DNA polymerase / Nucleotidyltransferase / Transferase / Transferase-DNA complex
Function / homology
Function and homology information


nucleoside binding / double-strand break repair via alternative nonhomologous end joining / hydrolase activity, acting on ester bonds / DNA-templated DNA replication / 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 / Taq DNA Polymerase; Chain T, domain 4 / 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 / Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / DNA polymerase 1 / 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
ACETATE ION / 4'-ethylthymidine 5'-(tetrahydrogen triphosphate) / DNA / DNA (> 10) / DNA polymerase I, thermostable
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDiederichs, K. / Marx, A. / Betz, K.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2010
Title: Structures of DNA polymerases caught processing size-augmented nucleotide probes.
Authors: Betz, K. / Streckenbach, F. / Schnur, A. / Exner, T. / Welte, W. / Diederichs, K. / Marx, A.
History
DepositionMar 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_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_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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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_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*(DOC))-3')
C: DNA (5'-D(*AP*AP*AP*AP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,54813
Polymers69,5033
Non-polymers4,04610
Water5,242291
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7640 Å2
ΔGint-17 kcal/mol
Surface area24370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.789, 108.789, 90.520
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-216-

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: polA, pol1 / Plasmid: pET-21b / 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 DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3')


Mass: 3617.371 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*AP*AP*AP*AP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')


Mass: 4948.217 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 6 types, 301 molecules

#4: Chemical ChemComp-HXZ / 4'-ethylthymidine 5'-(tetrahydrogen triphosphate)


Mass: 510.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H21N2O14P3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-15P / POLYETHYLENE GLYCOL (N=34) / PEG 1500 / Polyethylene glycol


Mass: 1529.829 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C69H140O35 / Comment: precipitant*YM
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 291 / 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: 2.22 Å3/Da / Density % sol: 44.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30% (w/v) PEG 8000, 0.2M ammonium acetate, 0.02M magnesium acetate, 0.05M sodium cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 800011
2ammonium acetate11
3magnesium acetate11
4sodium cacodylate11
5PEG 800012
6ammonium acetate12
7magnesium acetate12
8sodium cacodylate12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 13, 2009
Details: This noise-free counting device combines extraordinary spatial resolution with full frame read-out times of 5 ms. These features make it an ideal detector for PX and enable novel data ...Details: This noise-free counting device combines extraordinary spatial resolution with full frame read-out times of 5 ms. These features make it an ideal detector for PX and enable novel data acquisition modes such as continuos data acquisition and fine-phi-slicing.
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: 2→47.108 Å / Num. all: 42320 / Num. obs: 42216 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.97 % / Biso Wilson estimate: 40.828 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 22.1
Reflection shellResolution: 2→2.12 Å / Redundancy: 10.04 % / Rmerge(I) obs: 0.879 / Mean I/σ(I) obs: 2.59 / Num. unique all: 6678 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIXmodel building
PHENIX(phenix.refine: 1.6_289)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3KTQ

3ktq


Resolution: 2→47.107 Å / SU ML: 0.26 / Isotropic thermal model: isotropic and tls / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2207 2108 5 %RANDOM
Rwork0.1799 ---
all0.1819 42156 --
obs0.1819 42156 99.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.428 Å2 / ksol: 0.383 e/Å3
Displacement parametersBiso mean: 42.52 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: LAST / Resolution: 2→47.107 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4283 569 81 291 5224
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115095
X-RAY DIFFRACTIONf_angle_d0.8276990
X-RAY DIFFRACTIONf_dihedral_angle_d18.3951990
X-RAY DIFFRACTIONf_chiral_restr0.045760
X-RAY DIFFRACTIONf_plane_restr0.003806
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.04650.27991320.21592671X-RAY DIFFRACTION100
2.0465-2.09770.27111490.20942587X-RAY DIFFRACTION100
2.0977-2.15440.26331260.20612657X-RAY DIFFRACTION100
2.1544-2.21780.26321270.20332684X-RAY DIFFRACTION100
2.2178-2.28940.26961430.19732618X-RAY DIFFRACTION100
2.2894-2.37120.26461230.19542663X-RAY DIFFRACTION100
2.3712-2.46620.25361250.18552670X-RAY DIFFRACTION100
2.4662-2.57840.25181490.18812656X-RAY DIFFRACTION100
2.5784-2.71430.25621490.18672632X-RAY DIFFRACTION100
2.7143-2.88440.2141380.19312655X-RAY DIFFRACTION100
2.8844-3.1070.2361370.19422690X-RAY DIFFRACTION100
3.107-3.41960.20431490.18212663X-RAY DIFFRACTION100
3.4196-3.91420.18121590.15272679X-RAY DIFFRACTION100
3.9142-4.93070.17191410.13932708X-RAY DIFFRACTION100
4.9307-47.12010.19551610.17222815X-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)
11.83570.2153-0.27360.47450.17411.4930.0046-0.0029-0.3176-0.14410.0429-0.29290.45780.0647-0.02470.2936-0.04790.06490.1515-0.00360.316742.3739-43.0123-17.4846
20.87990.8684-0.35671.6693-0.20281.51430.1246-0.04930.10480.0928-0.1020.1074-0.3796-0.0726-0.03990.15570.00370.01240.147-0.00760.178533.4766-16.35351.1684
30.48970.8544-0.0770.5497-0.52432.5133-0.05790.07030.0443-0.03750.11150.0309-0.3786-0.4291-0.0860.17670.02210.02720.18480.00980.147430.0394-15.2837-9.7376
40.4231-0.0184-0.08810.8517-0.50782.3388-0.0498-0.13710.0670.10690.41620.2127-0.4222-1.3918-0.32560.26840.17590.05740.96270.16970.27889.7353-19.1361-3.6197
50.69920.0206-0.03620.46410.2491.1868-0.11750.1038-0.0239-0.21280.18450.0495-0.1507-0.5569-0.09910.2342-0.0333-0.00680.39880.05030.173522.156-22.8208-17.9673
60.34820.3239-1.09371.2783-0.96583.24910.01540.0456-0.12010.043-0.0162-0.0986-0.1830.0381-0.00250.1106-0.0009-0.02440.19790.02270.217634.5191-22.21182.4158
70.34240.43030.27660.61210.5782.814-0.2741-0.0245-0.1907-0.05360.1826-0.0826-0.1235-0.25740.07320.10640.0498-0.01150.22050.06210.142932.621-23.04376.3132
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 294:419)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 420:523)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 524:631)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 632:729)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 730:832)
6X-RAY DIFFRACTION6(CHAIN B)
7X-RAY DIFFRACTION7(CHAIN C)

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