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

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Basic information

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


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 polymerase family B signature. / DNA-directed DNA polymerase, family B, conserved site ...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 polymerase family B signature. / DNA-directed DNA polymerase, family B, conserved site / 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 / Helix Hairpins / Nucleotidyltransferase; domain 5 / 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-B9X / 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: 3.3 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 / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _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_conn_type.id
Revision 1.2Nov 6, 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*(DAL))-3')
D: DNA (5'-D(*AP*CP*TP*GP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,1427
Polymers100,4093
Non-polymers7344
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5340 Å2
ΔGint-49 kcal/mol
Surface area36040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)207.654, 207.654, 207.654
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 / 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*(DAL))-3')


Mass: 4256.766 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*AP*CP*TP*GP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*C)-3')


Mass: 5212.385 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 26 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.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-B9X / [(2R,3S,5R)-5-(6-aminopurin-9-yl)-2-(phosphonooxymethyl)oxolan-3-yl] 3-(2-ethoxyethoxy)propanoate


Mass: 475.390 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H26N5O9P
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 3.82 Å3/Da / Density % sol: 67.77 %
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: 0.9998 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Feb 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 3.3→48.99 Å / Num. obs: 21653 / % possible obs: 96.1 % / Redundancy: 1.9 % / CC1/2: 0.991 / Rmerge(I) obs: 0.04456 / Net I/σ(I): 6.73
Reflection shellResolution: 3.301→3.419 Å / Rmerge(I) obs: 0.47 / Num. unique obs: 2203 / CC1/2: 0.654

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSNovember 1, 2016 built20161205data reduction
SCALA3.3.22data scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K8X

4k8x


Resolution: 3.3→48.99 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.882 / SU B: 57.849 / SU ML: 0.432 / Cross valid method: THROUGHOUT / ESU R Free: 0.522 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27881 1129 5.2 %RANDOM
Rwork0.21538 ---
obs0.21867 20521 96.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 97.998 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 3.3→48.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5563 611 11 26 6211
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0126391
X-RAY DIFFRACTIONr_bond_other_d0.0010.0185214
X-RAY DIFFRACTIONr_angle_refined_deg1.1891.6078823
X-RAY DIFFRACTIONr_angle_other_deg1.1461.67611958
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6025756
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.59220.474274
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.24515766
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.3851542
X-RAY DIFFRACTIONr_chiral_restr0.0380.2866
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.027030
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021479
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_it1.2068.1583028
X-RAY DIFFRACTIONr_mcbond_other1.2058.1563026
X-RAY DIFFRACTIONr_mcangle_it2.17212.2353782
X-RAY DIFFRACTIONr_mcangle_other2.17212.2363783
X-RAY DIFFRACTIONr_scbond_it1.2328.5923363
X-RAY DIFFRACTIONr_scbond_other1.2318.5623354
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.19712.885029
X-RAY DIFFRACTIONr_long_range_B_refined6.6895.5037031
X-RAY DIFFRACTIONr_long_range_B_other6.67995.4777031
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.301→3.386 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.412 86 -
Rwork0.333 1535 -
obs--98.72 %
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)
11.60140.5344-0.55283.61630.55870.56280.54110.2301-0.2416-1.0267-0.65970.4314-0.4528-0.43040.11850.68530.3536-0.37730.3664-0.08830.3161-77.2645-9.2997-83.4664
20.6001-0.67830.32853.99740.50831.51190.12160.016-0.0326-0.152-0.07030.125-0.0345-0.0246-0.05120.1770.15580.02910.2281-0.0210.3334-60.792713.53-65.8705
30.419-0.52430.05011.25840.29340.5420.13280.0567-0.148-0.0912-0.2320.1623-0.02650.03990.09920.2322-0.0026-0.03180.2187-0.1040.3345-53.6903-25.5062-65.3637
42.5038-1.1134-0.00741.6344-0.13910.9976-0.0816-0.27110.19640.32420.0520.0904-0.3725-0.02060.02950.31190.0395-0.02760.1166-0.09040.2199-54.9471-3.9938-37.7679
51.62470.8264-1.19761.4282-1.02761.0752-0.0706-0.3404-0.78970.5041-0.30380.2833-0.18220.34990.37440.59370.07890.38760.37240.02460.8689-66.0427-18.2492-33.983
61.9463-0.2873-0.17893.32530.41830.06390.206-0.3947-0.2410.2778-0.34871.00450.03250.00570.14270.47640.22040.2260.70480.02950.3769-64.6726-18.6442-43.2557
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 152
2X-RAY DIFFRACTION2A153 - 323
3X-RAY DIFFRACTION3A324 - 611
4X-RAY DIFFRACTION4A612 - 757
5X-RAY DIFFRACTION5C-11 - 1
6X-RAY DIFFRACTION6D1 - 14

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