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- PDB-4dfm: Crystal structure of the large fragment of DNA polymerase I from ... -

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Basic information

Entry
Database: PDB / ID: 4dfm
TitleCrystal structure of the large fragment of DNA polymerase I from Thermus aquaticus in ternary complex with 5-(aminopentinyl)-2-dCTP
Components
  • 5'-d(AAAGCGCGCCGTGGTC)-3'
  • 5'-d(GACCACGGCGC ddG)-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-0L6 / FORMIC ACID / DNA / DNA (> 10) / DNA polymerase I, thermostable
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Difference Fourier Techniques / Resolution: 1.886 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_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: 5'-d(GACCACGGCGC ddG)-3'
C: 5'-d(AAAGCGCGCCGTGGTC)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,52214
Polymers69,5193
Non-polymers1,00411
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7610 Å2
ΔGint-14 kcal/mol
Surface area24680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.260, 108.260, 90.070
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-1062-

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 5'-d(GACCACGGCGC ddG)-3'


Mass: 3657.395 Da / Num. of mol.: 1 / Fragment: DNA Primer / Source method: obtained synthetically / Details: DNA synthesizer
#3: DNA chain 5'-d(AAAGCGCGCCGTGGTC)-3'


Mass: 4924.192 Da / Num. of mol.: 1 / Fragment: DNA Template / Source method: obtained synthetically / Details: DNA synthesizer

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Non-polymers , 5 types, 259 molecules

#4: Chemical ChemComp-0L6 / 5-(5-aminopent-1-yn-1-yl)-2'-deoxycytidine 5'-(tetrahydrogen triphosphate)


Mass: 550.289 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H25N4O13P3
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.88 %
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: X06DA / Wavelength: 0.99987 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 9, 2011
RadiationMonochromator: Bartels Monochromator, Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 1.886→47.15 Å / Num. all: 49434 / Num. obs: 48761 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Net I/σ(I): 12.77
Reflection shellResolution: 1.89→1.94 Å / Mean I/σ(I) obs: 1.83 / Num. unique all: 3643 / % possible all: 82

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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: 1.886→46.878 Å / SU ML: 0.23 / Isotropic thermal model: isotropic and tls / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 20.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2162 2442 5.01 %randoom
Rwork0.1859 ---
obs0.1875 48759 98.64 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.218 Å2 / ksol: 0.387 e/Å3
Displacement parametersBiso mean: 30.653 Å2
Baniso -1Baniso -2Baniso -3
1-9.3973 Å2-0 Å20 Å2
2--9.3973 Å20 Å2
3---2.3756 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 1.886→46.878 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4260 570 61 248 5139
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085078
X-RAY DIFFRACTIONf_angle_d0.9927150
X-RAY DIFFRACTIONf_dihedral_angle_d16.0411950
X-RAY DIFFRACTIONf_chiral_restr0.062765
X-RAY DIFFRACTIONf_plane_restr0.004804
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8863-1.92480.32221080.27182149X-RAY DIFFRACTION78
1.9248-1.96660.26991480.23122701X-RAY DIFFRACTION99
1.9666-2.01240.27531580.21322714X-RAY DIFFRACTION100
2.0124-2.06270.22641420.21062732X-RAY DIFFRACTION100
2.0627-2.11850.25431330.19962727X-RAY DIFFRACTION100
2.1185-2.18080.24251360.18372740X-RAY DIFFRACTION100
2.1808-2.25120.22721310.17852755X-RAY DIFFRACTION100
2.2512-2.33170.20211390.17712734X-RAY DIFFRACTION100
2.3317-2.4250.2461250.1772806X-RAY DIFFRACTION100
2.425-2.53540.20921500.18132715X-RAY DIFFRACTION100
2.5354-2.6690.25841520.18892759X-RAY DIFFRACTION100
2.669-2.83630.22771500.20592758X-RAY DIFFRACTION100
2.8363-3.05520.2461410.19412754X-RAY DIFFRACTION100
3.0552-3.36260.18991500.17892785X-RAY DIFFRACTION100
3.3626-3.8490.19141630.16752763X-RAY DIFFRACTION100
3.849-4.84850.18751530.16772814X-RAY DIFFRACTION100
4.8485-46.89240.21431630.19592911X-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)
11.9514-0.1383-0.16082.2130.03771.4836-0.0241-0.0628-0.3694-0.1854-0.0156-0.39550.25680.20180.05340.1644-0.03320.04090.11270.00760.202539.714-43.0274-17.6989
20.82690.53220.07871.07120.21281.1941-0.0055-0.10470.12520.00170.0230.035-0.36620.0609-0.01340.0893-0.03460.0210.04580.02150.080235.7819-12.6161-0.6895
31.64580.4780.08990.5855-1.07562.9445-0.0504-0.75420.5330.30740.1850.3336-0.9978-0.79210.0280.37810.20730.03890.5204-0.01810.257611.3627-13.7142-8.4485
40.7610.1190.32681.2125-0.29082.2956-0.2299-0.12370.2128-0.25630.05190.517-0.6449-0.8828-0.331-0.2217-0.06330.16290.06730.1507-0.082117.2208-24.8958-12.9819
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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