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- PDB-4dfp: Crystal structure of the large fragment of DNA Polymerase I from ... -

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Basic information

Entry
Database: PDB / ID: 4dfp
TitleCrystal structure of the large fragment of DNA Polymerase I from Thermus aqauticus in a ternary complex with 7-(aminopentinyl)-7-deaza-dGTP
Components
  • 5'-d(AAACGGCGCCGTGGTC)-3'
  • DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(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-0L7 / FORMIC ACID / DNA / DNA (> 10) / DNA polymerase I, thermostable
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Difference Fourier Techniques / Resolution: 2 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.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*(DOC))-3')
C: 5'-d(AAACGGCGCCGTGGTC)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,82021
Polymers69,4793
Non-polymers1,34118
Water5,008278
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8790 Å2
ΔGint-21 kcal/mol
Surface area24600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.448, 108.448, 90.435
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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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, UNP residues 293-831
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus aquaticus (bacteria) / Gene: polA, pol1 / 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 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 5'-d(AAACGGCGCCGTGGTC)-3'


Mass: 4924.192 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 5 types, 296 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: CH2O2
#7: Chemical ChemComp-0L7 / 2-amino-5-(5-aminopent-1-yn-1-yl)-7-{2-deoxy-5-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-erythro-pentofuranosyl}-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one


Mass: 587.309 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H24N5O13P3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 18% PEG 8000, 200mM Mg-Formate, 100 mM Tris 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: 0.9 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 12, 2011
RadiationMonochromator: LN2 cooled fixed-exit, Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2→46.959 Å / Num. all: 41869 / Num. obs: 41791 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Net I/σ(I): 12.36
Reflection shellResolution: 2→2.12 Å / Mean I/σ(I) obs: 1.69 / Num. unique all: 41869 / % possible all: 98.9

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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: 2→46.959 Å / SU ML: 0.28 / Isotropic thermal model: isotropic and tls / Cross valid method: THROUGHOUT / σ(F): 2.01 / Phase error: 22.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2239 2077 4.97 %random
Rwork0.185 ---
obs0.187 41788 99.83 %-
Solvent computationShrinkage radii: 1.24 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.298 Å2 / ksol: 0.355 e/Å3
Displacement parametersBiso mean: 38.627 Å2
Baniso -1Baniso -2Baniso -3
1-1.9033 Å2-0 Å2-0 Å2
2--1.9033 Å2-0 Å2
3----3.2458 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 2→46.959 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4264 567 83 278 5192
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095113
X-RAY DIFFRACTIONf_angle_d0.8367052
X-RAY DIFFRACTIONf_dihedral_angle_d15.7451962
X-RAY DIFFRACTIONf_chiral_restr0.048768
X-RAY DIFFRACTIONf_plane_restr0.003808
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.04660.31931340.27732592X-RAY DIFFRACTION98
2.0466-2.09780.32331310.24842598X-RAY DIFFRACTION100
2.0978-2.15450.25051250.22882622X-RAY DIFFRACTION100
2.1545-2.21790.28471250.20722660X-RAY DIFFRACTION100
2.2179-2.28950.25191390.19922601X-RAY DIFFRACTION100
2.2895-2.37130.26161240.19592663X-RAY DIFFRACTION100
2.3713-2.46620.26681210.19712628X-RAY DIFFRACTION100
2.4662-2.57850.241480.20022630X-RAY DIFFRACTION100
2.5785-2.71440.29731500.20222639X-RAY DIFFRACTION100
2.7144-2.88440.2431420.2092627X-RAY DIFFRACTION100
2.8844-3.10710.24941330.19682654X-RAY DIFFRACTION100
3.1071-3.41970.21721490.17922645X-RAY DIFFRACTION100
3.4197-3.91430.20021560.15562675X-RAY DIFFRACTION100
3.9143-4.93080.16371390.14992691X-RAY DIFFRACTION100
4.9308-46.97230.20331610.18622786X-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)
10.4267-0.48520.00310.91740.29040.3113-0.0753-0.0074-0.1031-0.1040.0328-0.10830.1550.051900.2381-0.02130.03430.20920.0120.247739.7928-43.2687-17.6018
20.44340.47240.04550.63340.14640.57640.0049-0.05330.017-0.0316-0.0240.0528-0.1324-0.0203-00.2159-0.00610.00120.1918-0.00160.208635.863-12.5088-0.7169
30.5265-0.17860.54260.5037-0.36370.4976-0.1405-0.24790.14410.19770.2156-0.034-0.5985-0.51830.05270.35290.1645-0.01770.4328-0.01970.202411.5947-13.8497-8.5376
40.35880.05620.15520.5968-0.32761.8608-0.1140.0123-0.0725-0.04710.13790.0595-0.1908-0.5015-0.20280.16940.0322-0.00270.26850.03430.176417.2609-24.9232-13.0888
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 604:685)
4X-RAY DIFFRACTION4chain 'A' and (resseq 686:832)

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