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- PDB-6isi: Structure of 9N-I DNA polymerase incorporation with 3'-CL in the ... -

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Basic information

Entry
Database: PDB / ID: 6isi
TitleStructure of 9N-I DNA polymerase incorporation with 3'-CL in the active site
Components
  • DNA (5'-D(P*AP*CP*GP*GP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')
  • DNA (5'-D(P*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*CP*CP*C)-3')
  • DNA polymerase
KeywordsTRANSFERASE/DNA / TRANSFERASE-DNA complex
Function / homology
Function and homology information


DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding
Similarity search - Function
DNA Polymerase; Chain A, domain 1 / DNA Polymerase, chain B, domain 1 / B family DNA polymerase, finger domain / Palm domain of DNA polymerase / B family DNA polymerase, palm domain / : / DNA polymerase family B, thumb domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B signature. ...DNA Polymerase; Chain A, domain 1 / DNA Polymerase, chain B, domain 1 / B family DNA polymerase, finger domain / Palm domain of DNA polymerase / B family DNA polymerase, palm domain / : / DNA polymerase family B, thumb domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B signature. / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Helix Hairpins / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-B0U / PYROPHOSPHATE / DNA / DNA (> 10) / DNA polymerase
Similarity search - Component
Biological speciesThermococcus sp. 9oN-7 (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsLinwu, S.W. / Maestre-Reyna, M. / Tsai, M.D. / Tu, Y.H. / Chang, W.H.
CitationJournal: Commun Biol / Year: 2019
Title: Thermococcus sp. 9°N DNA polymerase exhibits 3'-esterase activity that can be harnessed for DNA sequencing.
Authors: LinWu, S.W. / Tu, Y.H. / Tsai, T.Y. / Maestre-Reyna, M. / Liu, M.S. / Wu, W.J. / Huang, J.Y. / Chi, H.W. / Chang, W.H. / Chiou, C.F. / Wang, A.H. / Lee, J. / Tsai, M.D.
History
DepositionNov 16, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase
C: DNA (5'-D(P*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*CP*CP*C)-3')
D: DNA (5'-D(P*AP*CP*GP*GP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,6129
Polymers101,0523
Non-polymers5606
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-75 kcal/mol
Surface area35380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)205.204, 205.204, 205.204
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA polymerase


Mass: 90939.820 Da / Num. of mol.: 1 / Fragment: UNP residues 1-775 / Mutation: D141A, E143A, A485L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus sp. 9oN-7 (archaea) / Strain: 9oN-7 / Gene: pol, polA
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q56366, DNA-directed DNA polymerase

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DNA chain , 2 types, 2 molecules CD

#2: DNA chain DNA (5'-D(P*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*CP*CP*C)-3')


Mass: 4545.948 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*AP*CP*GP*GP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')


Mass: 5566.604 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 27 molecules

#4: Chemical ChemComp-PPV / PYROPHOSPHATE


Mass: 177.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4O7P2
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-B0U / 3-[2-[2-(2-azanylethoxy)ethoxy]ethoxy]propanoic acid


Mass: 221.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H19NO5
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.67 Å3/Da / Density % sol: 66.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: Sodium Acetate pH4.6, MPD, Glycerol, CaCl2

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jun 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→40.24 Å / Num. obs: 23807 / % possible obs: 99.85 % / Redundancy: 2 % / CC1/2: 0.99 / Rmerge(I) obs: 0.024 / Net I/σ(I): 9.12
Reflection shellResolution: 3.2→3.314 Å / Rmerge(I) obs: 0.41 / Num. unique obs: 2372 / CC1/2: 0.71

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSNovember 1, 2016 built 20161205data reduction
SCALA3.3.22data scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K8X

4k8x


Resolution: 3.2→40.24 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.876 / SU B: 54.794 / SU ML: 0.421 / Cross valid method: THROUGHOUT / ESU R Free: 0.493
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29019 1243 5.2 %RANDOM
Rwork0.23188 ---
obs0.23492 22579 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 106.389 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 3.2→40.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5505 573 28 24 6130
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0126303
X-RAY DIFFRACTIONr_bond_other_d0.0010.0185096
X-RAY DIFFRACTIONr_angle_refined_deg1.2741.68709
X-RAY DIFFRACTIONr_angle_other_deg1.2271.67411702
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5995756
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.8721.429259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.12215740
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5191533
X-RAY DIFFRACTIONr_chiral_restr0.0480.2858
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026970
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021420
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3745.3143027
X-RAY DIFFRACTIONr_mcbond_other1.3745.3133026
X-RAY DIFFRACTIONr_mcangle_it2.4717.9693782
X-RAY DIFFRACTIONr_mcangle_other2.4717.9713783
X-RAY DIFFRACTIONr_scbond_it1.9325.7753276
X-RAY DIFFRACTIONr_scbond_other1.9325.7773277
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3228.6784928
X-RAY DIFFRACTIONr_long_range_B_refined6.78963.1767252
X-RAY DIFFRACTIONr_long_range_B_other6.78963.197253
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 85 -
Rwork0.351 1648 -
obs--100 %
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)
10.3380.04620.16323.26770.78210.31590.2936-0.03030.0207-0.3963-0.25180.177-0.0842-0.1653-0.04180.71410.2526-0.09030.7441-0.08060.7015-66.7332.613-72.895
20.6568-0.73560.21451.44210.23510.9239-0.07880.0675-0.0550.2428-0.20790.0956-0.06450.00620.28660.6957-0.0505-0.01770.6251-0.15250.8228-52.882-19.483-54.742
30.7898-0.63632.70427.0415-22.578591.0394-1.6091-0.0778-0.05071.8505-3.3679-1.2863-9.28213.27174.9772.43610.43070.15283.5071-0.23292.4709-67.478-20.262-25.371
418.908-6.7174-6.2418.1514.7693.2721-0.2907-0.663-0.18930.7776-0.0360.16680.4142-0.03150.32670.959-0.0029-0.00950.9842-0.11780.6431-59.798-15.73-47.825
51.5702-1.4559-0.16782.38280.08020.355-0.0369-0.1638-0.16880.3374-0.21110.6716-0.0529-0.45230.2480.7747-0.00150.08711.0703-0.30520.8753-60.941-19.373-49.796
69.8311-3.4616-6.666930.807913.86729.0239-2.6975-0.91220.38281.69361.82692.89562.06731.29970.87061.79450.36530.67072.13030.09080.808-69.707-15.192-30.021
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 346
2X-RAY DIFFRACTION2A347 - 757
3X-RAY DIFFRACTION3C-10 - -5
4X-RAY DIFFRACTION4C-4 - 2
5X-RAY DIFFRACTION5D1 - 9
6X-RAY DIFFRACTION6D10 - 14

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