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- PDB-3sv3: Crystal structure of the large fragment of DNA polymerase I from ... -

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Basic information

Entry
Database: PDB / ID: 3sv3
TitleCrystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in a closed ternary complex with the artificial base pair dNaM-d5SICSTP
Components
  • (5'-D(*AP*AP*AP*(BMN)P*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')
  • (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3')
  • DNA polymerase I, thermostable
KeywordsTRANSFERASE/DNA / DNA polymerase / artificial base pair / TRANSFERASE-DNA complex
Function / homology
Function and homology information


nucleoside binding / hydrolase activity, acting on ester bonds / double-strand break repair via alternative nonhomologous end joining / 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
Chem-5SI / FORMIC ACID / DNA / DNA (> 10) / DNA polymerase I, thermostable
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsBetz, K. / Diederichs, K. / Marx, A.
CitationJournal: Nat.Chem.Biol. / Year: 2012
Title: KlenTaq polymerase replicates unnatural base pairs by inducing a Watson-Crick geometry.
Authors: Betz, K. / Malyshev, D.A. / Lavergne, T. / Welte, W. / Diederichs, K. / Dwyer, T.J. / Ordoukhanian, P. / Romesberg, F.E. / Marx, A.
History
DepositionJul 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 4, 2012Group: Database references
Revision 1.2Sep 12, 2012Group: Database references
Revision 1.3Sep 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_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: (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3')
C: (5'-D(*AP*AP*AP*(BMN)P*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,81530
Polymers69,5263
Non-polymers2,28927
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9130 Å2
ΔGint-47 kcal/mol
Surface area25190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.545, 108.545, 90.978
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 293-832
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus aquaticus (bacteria) / Gene: pol I, pol1, polA / 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(*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 / Details: DNA synthesizer
#3: DNA chain (5'-D(*AP*AP*AP*(BMN)P*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')


Mass: 4971.287 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA synthesizer

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Non-polymers , 5 types, 268 molecules

#4: Chemical ChemComp-5SI / 2-{2-deoxy-5-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-erythro-pentofuranosyl}-6-methylisoquinoline-1(2H)-thione


Mass: 531.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H20NO12P3S
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: CH2O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 2.23 Å3/Da / Density % sol: 44.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 13% PEG 8000, 100mM NH4Cl, 0.1M MgFormate, 0.1M 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: 0.9999 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 17, 2010
RadiationMonochromator: LN2 cooled fixed-exit Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.1→47 Å / Num. all: 36595 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.98 % / Net I/σ(I): 12.41
Reflection shellResolution: 2.1→2.23 Å / Mean I/σ(I) obs: 2.33 / Num. unique all: 5822 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.7.1_743)model building
PHENIX(phenix.refine: 1.7.1_743)refinement
XDSdata reduction
XDSdata scaling
PHENIX1.7.1_743phasing
RefinementStarting model: PDB ENTRY 3M8S

3m8s


Resolution: 2.1→47.001 Å / SU ML: 0.55 / σ(F): 1.2 / Phase error: 22.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2154 3511 5.02 %random
Rwork0.1673 ---
obs0.1698 69989 99.97 %-
all-70010 --
Solvent computationShrinkage radii: 0.65 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.717 Å2 / ksol: 0.415 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.219 Å20 Å2-0 Å2
2--2.219 Å2-0 Å2
3----4.4381 Å2
Refinement stepCycle: LAST / Resolution: 2.1→47.001 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4291 511 141 241 5184
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085123
X-RAY DIFFRACTIONf_angle_d1.1447034
X-RAY DIFFRACTIONf_dihedral_angle_d17.481969
X-RAY DIFFRACTIONf_chiral_restr0.057762
X-RAY DIFFRACTIONf_plane_restr0.005813
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1001-2.12880.30581230.26552659X-RAY DIFFRACTION99
2.1288-2.15920.29141320.24752687X-RAY DIFFRACTION100
2.1592-2.19150.30461390.24612627X-RAY DIFFRACTION100
2.1915-2.22570.28211040.24522712X-RAY DIFFRACTION100
2.2257-2.26220.28521350.22522708X-RAY DIFFRACTION100
2.2622-2.30120.27871480.22762615X-RAY DIFFRACTION100
2.3012-2.34310.25641300.21552652X-RAY DIFFRACTION100
2.3431-2.38810.30441160.22272709X-RAY DIFFRACTION100
2.3881-2.43690.29141280.22412665X-RAY DIFFRACTION100
2.4369-2.48990.31761270.22232680X-RAY DIFFRACTION100
2.4899-2.54780.28671670.20752591X-RAY DIFFRACTION100
2.5478-2.61150.25381450.18992692X-RAY DIFFRACTION100
2.6115-2.68210.23221390.17092655X-RAY DIFFRACTION100
2.6821-2.7610.21031440.18032644X-RAY DIFFRACTION100
2.761-2.85010.26141540.17172660X-RAY DIFFRACTION100
2.8501-2.9520.25481530.15862648X-RAY DIFFRACTION100
2.952-3.07010.19231250.15082695X-RAY DIFFRACTION100
3.0701-3.20980.19641500.15132627X-RAY DIFFRACTION100
3.2098-3.3790.17741380.14882659X-RAY DIFFRACTION100
3.379-3.59060.18571530.13672664X-RAY DIFFRACTION100
3.5906-3.86780.20511710.13552620X-RAY DIFFRACTION100
3.8678-4.25670.15911690.12632623X-RAY DIFFRACTION100
4.2567-4.87220.19191200.12392686X-RAY DIFFRACTION100
4.8722-6.13630.19341460.17172645X-RAY DIFFRACTION100
6.1363-47.01310.20551550.18152655X-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)
13.785-0.1503-0.76562.8593-0.1331.9876-0.09780.1085-0.3765-0.27550.0207-0.25860.26760.19560.06020.2944-0.03530.02890.1905-0.01410.232939.7265-43.1657-17.776
20.86530.67590.53511.64621.22572.9146-0.0415-0.04250.1397-0.1226-0.00790.0527-0.4408-0.0430.04560.18730.00310.00240.13670.02320.215435.8455-12.5877-0.7615
31.31110.16990.31170.6569-0.57692.4713-0.1524-0.87190.56960.45530.23240.0165-1.4093-0.88830.03770.68920.2553-0.0570.5565-0.11530.025411.1774-14.0605-7.9487
41.57430.3617-0.00011.7939-0.68583.8575-0.0419-0.0677-0.01530.00540.05210.1566-0.3888-0.5426-0.04350.20330.0216-0.0320.2388-0.01690.182617.4324-25.3356-13.63
53.02321.7948-0.04791.25980.31661.61890.0270.1758-0.22740.1068-0.2148-0.317-0.04560.6830.12110.22180.0487-0.0220.31060.0030.342736.8617-22.91074.4011
60.85911.7937-0.5214.23530.16963.2258-0.2855-0.08470.1080.23510.0955-0.1588-0.016-0.01210.22270.21540.0860.01350.2465-0.01840.160335.8528-23.8135.303
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 293:433)
2X-RAY DIFFRACTION2(chain A and resid 434:603)
3X-RAY DIFFRACTION3(chain A and resid 604:687)
4X-RAY DIFFRACTION4(chain A and resid 688:832)
5X-RAY DIFFRACTION5(chain B and resid 101:112)
6X-RAY DIFFRACTION6(chain C and resid 204:216)

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