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- PDB-4df8: Crystal structure of the large fragment of DNA Polymerase I from ... -

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Basic information

Entry
Database: PDB / ID: 4df8
TitleCrystal structure of the large fragment of DNA Polymerase I from Thermus aquaticus in a closed ternary complex with aminopentinyl-7-deaza-2-dATP
Components
  • DNA (5'-D(*AP*AP*AP*TP*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 Polymerase / TRANSFERASE-DNA complex
Function / homology
Function and homology information


nucleoside binding / hydrolase activity, acting on ester bonds / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA repair / 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
Chem-0L4 / 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 23, 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_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_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_seq_id / _struct_conn.ptnr2_label_asym_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*TP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,64117
Polymers69,4943
Non-polymers1,14814
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8180 Å2
ΔGint-31 kcal/mol
Surface area24700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.609, 108.609, 90.516
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
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 DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3')


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


Mass: 4939.203 Da / Num. of mol.: 1 / Fragment: DNA Template / Source method: obtained synthetically / Details: DNA synthesizer

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Non-polymers , 6 types, 217 molecules

#4: Chemical ChemComp-0L4 / 5-(5-aminopent-1-yn-1-yl)-7-{2-deoxy-5-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-erythro-pentofuranosyl}-7H-pyrrolo[2,3-d]pyrimidin-4-amine


Mass: 571.309 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H24N5O12P3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#8: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 44.54 %
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

Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.23 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationMonochromator: Bartels Monochromator Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.23 Å / Relative weight: 1
ReflectionResolution: 2→47.03 Å / Num. all: 42038 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Net I/σ(I): 14.43
Reflection shellResolution: 2→2.12 Å / Mean I/σ(I) obs: 1.78 / Num. unique all: 6661 / % possible all: 99.4

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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→47.029 Å / SU ML: 0.3 / Isotropic thermal model: isotropic and tls / Cross valid method: THROUGHOUT / σ(F): 1.26 / Phase error: 24.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2339 4047 5.02 %random
Rwork0.1946 ---
obs0.1966 80633 99.9 %-
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.93 Å2 / ksol: 0.344 e/Å3
Displacement parametersBiso mean: 35.99 Å2
Baniso -1Baniso -2Baniso -3
1-8.0089 Å20 Å2-0 Å2
2--8.0089 Å2-0 Å2
3----6.5238 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2→47.029 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4282 568 69 203 5122
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0145093
X-RAY DIFFRACTIONf_angle_d0.9937019
X-RAY DIFFRACTIONf_dihedral_angle_d17.5321963
X-RAY DIFFRACTIONf_chiral_restr0.05765
X-RAY DIFFRACTIONf_plane_restr0.004807
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02360.42561500.36742578X-RAY DIFFRACTION97
2.0236-2.04820.30111270.33032707X-RAY DIFFRACTION100
2.0482-2.07420.35551360.29132523X-RAY DIFFRACTION100
2.0742-2.10150.28291370.27482690X-RAY DIFFRACTION100
2.1015-2.13020.26721260.25982666X-RAY DIFFRACTION100
2.1302-2.16070.28511280.24842664X-RAY DIFFRACTION100
2.1607-2.19290.30251430.24312588X-RAY DIFFRACTION100
2.1929-2.22720.29621010.2392691X-RAY DIFFRACTION100
2.2272-2.26370.2691430.22342706X-RAY DIFFRACTION100
2.2637-2.30270.2631520.22122595X-RAY DIFFRACTION100
2.3027-2.34460.2411230.20972650X-RAY DIFFRACTION100
2.3446-2.38970.27691030.21392676X-RAY DIFFRACTION100
2.3897-2.43850.2891300.21312671X-RAY DIFFRACTION100
2.4385-2.49150.28111300.20912626X-RAY DIFFRACTION100
2.4915-2.54950.24431610.20222611X-RAY DIFFRACTION100
2.5495-2.61320.26961530.21082692X-RAY DIFFRACTION100
2.6132-2.68390.33031360.22872584X-RAY DIFFRACTION100
2.6839-2.76280.25411420.21612686X-RAY DIFFRACTION100
2.7628-2.8520.25871560.20962620X-RAY DIFFRACTION100
2.852-2.95390.25351550.20492626X-RAY DIFFRACTION100
2.9539-3.07210.2991210.20572674X-RAY DIFFRACTION100
3.0721-3.21190.23221460.18882649X-RAY DIFFRACTION100
3.2119-3.38120.20051400.17862621X-RAY DIFFRACTION100
3.3812-3.5930.19251470.1722624X-RAY DIFFRACTION100
3.593-3.87030.22211710.16152620X-RAY DIFFRACTION100
3.8703-4.25960.16641720.1582598X-RAY DIFFRACTION100
4.2596-4.87540.23231170.14642679X-RAY DIFFRACTION100
4.8754-6.14030.2071470.17722635X-RAY DIFFRACTION100
6.1403-47.04210.17441540.16342636X-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)
10.1542-0.10270.04320.33790.18750.2096-0.0287-0.0452-0.1595-0.13250.0154-0.09920.15940.0553-0.0010.1903-0.03130.04340.1476-00.230940.0521-43.0445-17.7416
20.38810.42770.09910.5216-0.06150.30680.0161-0.0530.020.0152-0.03120.0308-0.1708-0.0045-0.02940.1906-0.03360.02650.1328-0.01080.154535.8451-12.5349-0.7127
30.28940.12340.12270.5746-0.00580.4609-0.3899-0.09570.0014-0.01450.31210.0018-0.528-0.64160.00010.220.2691-0.0520.40150.03580.136711.4949-14.0035-8.5233
40.2781-0.07280.30060.56010.03580.8623-0.122-0.0669-0.0875-0.08930.08270.0135-0.3256-0.5119-0.25230.0722-0.01640.00950.2820.05980.128817.2552-25.0954-13.1788
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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