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- PDB-6is7: Structure of 9N-I DNA polymerase incorporation with dA in the act... -

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Basic information

Entry
Database: PDB / ID: 6is7
TitleStructure of 9N-I DNA polymerase incorporation with dA in the active site
Components
  • DNA (5'-D(*AP*CP*TP*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*A)-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
DNA / DNA (> 10) / DNA polymerase
Similarity search - Component
Biological speciesThermococcus sp. 9oN-7 (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 15, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Oct 23, 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
B: DNA polymerase
C: DNA (5'-D(P*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*CP*CP*A)-3')
D: DNA (5'-D(*AP*CP*TP*GP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')
E: DNA (5'-D(P*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*CP*CP*A)-3')
F: DNA (5'-D(*AP*CP*TP*GP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')
I: DNA (5'-D(*AP*CP*TP*GP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')
K: DNA (5'-D(P*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*CP*CP*A)-3')
L: DNA (5'-D(P*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*CP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,06516
Polymers216,7849
Non-polymers2817
Water3,819212
1
A: DNA polymerase
C: DNA (5'-D(P*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*CP*CP*A)-3')
D: DNA (5'-D(*AP*CP*TP*GP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')
I: DNA (5'-D(*AP*CP*TP*GP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')
K: DNA (5'-D(P*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*CP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,2437
Polymers111,1635
Non-polymers802
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA polymerase
E: DNA (5'-D(P*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*CP*CP*A)-3')
F: DNA (5'-D(*AP*CP*TP*GP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')
L: DNA (5'-D(P*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*CP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,8229
Polymers105,6214
Non-polymers2005
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.951, 106.767, 255.903
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22E
13D
23F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETLEULEUAA1 - 7551 - 755
21METMETLEULEUBB1 - 7551 - 755
12DGDGDADACC-12 - 21 - 15
22DGDGDADAEE-12 - 21 - 15
13DADADGDGDD1 - 181 - 18
23DADADGDGFF1 - 181 - 18

NCS ensembles :
ID
1
2
3

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Components

#1: Protein DNA polymerase


Mass: 90939.820 Da / Num. of mol.: 2 / 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
#2: DNA chain
DNA (5'-D(P*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*CP*CP*A)-3')


Mass: 4569.973 Da / Num. of mol.: 4 / 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*CP*G)-3')


Mass: 5541.591 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O
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: 3.15 Å3/Da / Density % sol: 60.99 %
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: Nov 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 2.8→46.29 Å / Num. obs: 63508 / % possible obs: 99.41 % / Redundancy: 2 % / CC1/2: 0.994 / Rmerge(I) obs: 0.04708 / Net I/σ(I): 1.88
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.335 / Num. unique obs: 6242 / CC1/2: 0.703

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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: 2.8→46.29 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.859 / SU B: 33.444 / SU ML: 0.326 / Cross valid method: THROUGHOUT / ESU R: 0.928 / ESU R Free: 0.372 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27625 3139 5 %RANDOM
Rwork0.22493 ---
obs0.22748 60118 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 81.663 Å2
Baniso -1Baniso -2Baniso -3
1--1.59 Å20 Å2-0 Å2
2---2.78 Å2-0 Å2
3---4.37 Å2
Refinement stepCycle: 1 / Resolution: 2.8→46.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11606 1564 7 245 13422
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01213628
X-RAY DIFFRACTIONr_bond_other_d0.0010.01711712
X-RAY DIFFRACTIONr_angle_refined_deg1.2251.58318821
X-RAY DIFFRACTIONr_angle_other_deg1.1511.68426951
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.14951511
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.96120.904586
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.782151850
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1531587
X-RAY DIFFRACTIONr_chiral_restr0.0480.21806
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214417
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023067
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_it1.0024.1476050
X-RAY DIFFRACTIONr_mcbond_other1.0024.1476049
X-RAY DIFFRACTIONr_mcangle_it1.8176.2197559
X-RAY DIFFRACTIONr_mcangle_other1.8176.2197560
X-RAY DIFFRACTIONr_scbond_it0.9614.0087578
X-RAY DIFFRACTIONr_scbond_other0.9614.0077577
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7495.99811263
X-RAY DIFFRACTIONr_long_range_B_refined4.62844.1614989
X-RAY DIFFRACTIONr_long_range_B_other4.62844.15814988
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A222410.07
12B222410.07
21C12810.05
22E12810.05
31D14400.07
32F14400.07
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 252 -
Rwork0.31 4354 -
obs--98.93 %
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)
11.75890.26890.09786.4361-0.66561.9514-0.1331-0.2083-0.07590.16870.0560.71690.1906-0.43550.07710.62260.0534-0.10840.6059-0.10050.1871-24.226121.61240.586
23.8326-0.91040.30983.41310.29931.963-0.0568-0.21650.49570.05650.0293-0.1044-0.40550.03320.02740.83490.1009-0.23390.4702-0.05410.1852-4.19152.42246.342
31.98-0.26941.39450.8220.24231.4359-0.06680.0158-0.08860.05690.0893-0.04260.04440.0539-0.02250.76880.1213-0.13070.5013-0.06340.06312.237121.00141.124
43.6136-0.96160.73441.1312-0.22922.14960.09660.3957-0.2555-0.4260.0647-0.09290.10010.3569-0.16120.66470.0998-0.06880.4838-0.18820.105813.511114.57435.702
54.87260.4483-0.38973.43220.36774.26590.0616-0.04110.21440.18250.03-0.413-0.3720.4002-0.09160.7605-0.0068-0.22260.4604-0.07190.196222.894138.64160.674
66.47780.3341-1.11762.1245-0.37522.2693-0.11390.04830.34210.14840.0893-0.04-0.37840.0710.02450.61660.0317-0.01540.433-0.16060.132955.323204.1225.405
77.13620.36032.42452.60571.48892.84240.1609-0.2212-0.1296-0.26270.09960.9543-0.2543-0.6917-0.26050.87120.1447-0.07750.79010.10211.002717.116192.08319.331
81.3060.00031.67973.05931.13123.09680.178-0.2495-0.1796-0.3308-0.09721.126-0.0624-0.4107-0.08080.75730.1733-0.04640.6304-0.0480.587429.372186.07620.009
91.2492-0.1822-0.32545.3131-0.04991.35280.2435-0.309-0.12420.28360.0634-0.26170.11240.0952-0.30690.57510.0923-0.20780.551-0.07550.159158.61169.31328.978
102.9328-0.02420.70571.47550.583.29040.1788-0.015-0.3887-0.12970.09050.04640.3338-0.4509-0.26930.63880.0668-0.20450.5214-0.08940.181435.07159.2427.649
118.12557.6829-0.819629.34985.76918.93231.38390.08360.7609-0.36020.8021-1.4903-1.10150.1442-2.18590.7078-0.00310.08870.65570.02860.62329.326122.96981.327
1211.1554-1.7508-0.606611.2702-4.56832.02370.1073-0.1589-1.08090.01970.20240.96960.0666-0.0697-0.30960.61380.0236-0.21550.4792-0.03340.239416.294122.19266.772
1310.1163-3.9611-5.35325.08981.0982.87590.78810.75171.4125-0.2398-0.0791-1.6937-0.3987-0.405-0.7090.50420.1139-0.10030.5446-0.01220.363115.927125.18649.065
1428.1756-4.37871.03570.73130.18943.28220.5293-0.66960.0409-0.09180.1046-0.0415-0.5320.2323-0.63390.6801-0.01130.04610.4961-0.08910.33875.213120.82449.953
1525.67728.216-1.64227.43013.10430.64060.5069-0.4939-0.7719-1.5284-0.3292-1.892-0.3244-0.0195-0.17770.69990.069-0.07940.50980.00580.186419.467120.3556.023
165.91530.6614-5.145513.2034-0.996.43720.6075-0.29930.16060.65840.20511.3212-0.57550.274-0.81270.5228-0.0243-0.11930.52280.0530.437819.78125.53973.167
170.7303-1.3392-0.854810.43310.2251.6325-0.1933-0.434-0.2157-0.51320.2116-0.4686-0.10010.743-0.01831.01810.06250.26350.86960.01911.011332.493115.15983.528
1819.0489-1.4666.50113.7722-2.923213.73550.8053-0.27190.16440.03720.20241.35660.15460.3958-1.00780.62480.03980.12330.5322-0.08240.570746.995154.595-20.84
199.75975.31952.881323.65827.95227.78440.0561-0.3923-0.38730.07130.0357-0.99990.09050.1992-0.09170.54080.0042-0.01050.5399-0.07890.271352.718158.388-6.881
204.0643-3.1347-1.04549.1135-2.93984.35570.35260.21060.00290.00260.48720.3113-0.024-0.0435-0.83980.50780.0498-0.10860.3826-0.14540.254147.417166.6599.968
210.9745-2.52891.371624.5022-2.48952.64310.26930.14660.2723-0.8658-0.29880.46410.4373-0.2440.02950.61620.07970.02740.65940.12990.58152.737174.82515.28
2212.69411.90698.15552.87560.45125.50010.32810.0536-0.53110.23510.10460.22270.2689-0.0467-0.43280.59680.0264-0.09850.4894-0.15670.137348.727160.9045.7
2311.7758-4.1539-2.99362.5437-1.00444.7364-0.02410.45921.4637-0.12950.2181-0.64560.1594-0.75-0.19410.6762-0.03990.1130.6797-0.1970.354749.078163.196-11.805
245.9646-7.5182-0.22569.94110.440.06470.70320.28020.6074-0.7744-0.4538-1.4231-0.0384-0.066-0.24930.82420.01170.09850.739-0.04251.105858.076151.572-21.728
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 129
2X-RAY DIFFRACTION2A130 - 326
3X-RAY DIFFRACTION3A327 - 408
4X-RAY DIFFRACTION4A409 - 605
5X-RAY DIFFRACTION5A606 - 757
6X-RAY DIFFRACTION6B1 - 135
7X-RAY DIFFRACTION7B136 - 208
8X-RAY DIFFRACTION8B209 - 349
9X-RAY DIFFRACTION9B350 - 577
10X-RAY DIFFRACTION10B578 - 756
11X-RAY DIFFRACTION11C-12 - -8
12X-RAY DIFFRACTION12C-7 - -2
13X-RAY DIFFRACTION13C-1 - 2
14X-RAY DIFFRACTION14D1 - 4
15X-RAY DIFFRACTION15D5 - 8
16X-RAY DIFFRACTION16D9 - 14
17X-RAY DIFFRACTION17D15 - 18
18X-RAY DIFFRACTION18E-12 - -9
19X-RAY DIFFRACTION19E-8 - -5
20X-RAY DIFFRACTION20E-4 - 2
21X-RAY DIFFRACTION21F1 - 4
22X-RAY DIFFRACTION22F5 - 10
23X-RAY DIFFRACTION23F11 - 14
24X-RAY DIFFRACTION24F15 - 18

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