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- PDB-4df4: Crystal structure of the large fragment of DNA Polymerase I from ... -

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Basic information

Entry
Database: PDB / ID: 4df4
TitleCrystal structure of the large fragment of DNA Polymerase I from Thermus aquaticus in a closed ternary complex with 7-(N-(10-hydroxydecanoyl)-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 / 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-0L3 / DNA / DNA (> 10) / DNA polymerase I, thermostable
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Difference Fourier Techniques / Resolution: 2.2 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 / pdbx_struct_special_symmetry / 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_alt_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_alt_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.pdbx_ptnr1_label_alt_id / _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: 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)70,41910
Polymers69,4943
Non-polymers9257
Water6,413356
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5720 Å2
ΔGint-37 kcal/mol
Surface area24930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.815, 107.815, 89.678
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-905-

MG

21A-1225-

HOH

31A-1296-

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 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
#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

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Non-polymers , 4 types, 363 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-0L3 / 7-{2-deoxy-5-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-erythro-pentofuranosyl}-5-{5-[(10-hydroxydecanoyl)amino]pent-1-yn-1-yl}-7H-pyrrolo[2,3-d]pyrimidin-4-amine


Mass: 741.558 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H42N5O14P3
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / 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: 2.17 Å3/Da / Density % sol: 43.19 %
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: X06DA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 12, 2011
RadiationMonochromator: Bartels Monochromator Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→46.7 Å / Num. all: 41667 / Num. obs: 41455 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11.09 % / Net I/σ(I): 13.87
Reflection shellResolution: 1.99→2.11 Å / Mean I/σ(I) obs: 1.64 / Num. unique all: 6441 / % possible all: 96.9

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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: 2.2→46.202 Å / SU ML: 0.28 / Isotropic thermal model: isotropic and tls / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 21.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2269 1568 5.07 %RANDOM
Rwork0.1775 ---
obs0.18 30932 99.99 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 14.871 Å2 / ksol: 0.317 e/Å3
Displacement parametersBiso mean: 25.27 Å2
Baniso -1Baniso -2Baniso -3
1-13.294 Å20 Å20 Å2
2--13.294 Å20 Å2
3---8.0678 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 2.2→46.202 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4276 508 57 356 5197
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115048
X-RAY DIFFRACTIONf_angle_d0.8216966
X-RAY DIFFRACTIONf_dihedral_angle_d15.2281958
X-RAY DIFFRACTIONf_chiral_restr0.046759
X-RAY DIFFRACTIONf_plane_restr0.003811
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.27110.28991380.21392622X-RAY DIFFRACTION100
2.2711-2.35230.24621260.2082665X-RAY DIFFRACTION100
2.3523-2.44650.32011230.21232640X-RAY DIFFRACTION100
2.4465-2.55780.26431500.20362661X-RAY DIFFRACTION100
2.5578-2.69260.28651500.19892621X-RAY DIFFRACTION100
2.6926-2.86130.25621370.20352647X-RAY DIFFRACTION100
2.8613-3.08220.25031340.19832671X-RAY DIFFRACTION100
3.0822-3.39230.22941490.18692658X-RAY DIFFRACTION100
3.3923-3.8830.20381590.162669X-RAY DIFFRACTION100
3.883-4.89120.17951410.14142707X-RAY DIFFRACTION100
4.8912-46.21260.20471610.16612803X-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)
10.06760.0261-0.00850.0319-0.0140.0761-0.0182-0.0025-0.1523-0.0822-0.0021-0.1150.1260.0419-0.01630.07920.01950.00060.01830.02230.13439.9181-42.8681-17.8547
20.08850.073-0.02180.0539-0.04530.0440.0546-0.0460.09660.0546-0.047-0.0131-0.0365-0.06310.0029-0.042-0.12680.0589-0.04990.02930.028131.7371-13.5691-3.2747
30.0466-0.01210.01530.00620.00720.0397-0.0194-0.1270.03670.06270.05550.0286-0.154-0.224-0.01190.21680.06990.01790.21920.02090.10049.4136-21.368-2.4503
40.0747-0.03090.05130.09890.07720.15980.0111-0.031-0.0275-0.08050.040.0025-0.0594-0.09560.07780.0222-0.0125-0.01840.03950.00970.023822.6604-21.3904-19.8321
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 294:433)
2X-RAY DIFFRACTION2chain 'A' and (resseq 434:633)
3X-RAY DIFFRACTION3chain 'A' and (resseq 634:737)
4X-RAY DIFFRACTION4chain 'A' and (resseq 738:832)

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