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- PDB-6q4t: KOD DNA pol in a closed ternary complex with 7-deaza-7-(2-(2-hydr... -

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Basic information

Entry
Database: PDB / ID: 6q4t
TitleKOD DNA pol in a closed ternary complex with 7-deaza-7-(2-(2-hydroxyethoxy)-N-(prop-2-yn-1-yl)acetamide)-2-dATP
Components
  • DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*CP*AP*C)-3')
  • DNA (5'-D(P*AP*AP*CP*TP*GP*TP*GP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')
  • DNA polymerase,DNA polymerase,DNA polymerase
KeywordsDNA BINDING PROTEIN / DNA polymerase archaeal B-family modified nucleotide next-generation sequencing
Function / homology
Function and homology information


intron homing / intein-mediated protein splicing / exonuclease activity / DNA-templated DNA replication / endonuclease activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding
Similarity search - Function
DNA polymerase II intein domain IV / DNA polymerase II intein Domain IV / LAGLIDADG-like domain / Intein splicing domain / Intein / Intein DOD homing endonuclease / Intein DOD-type homing endonuclease domain profile. / DNA Polymerase; Chain A, domain 1 / DNA Polymerase, chain B, domain 1 / Intein C-terminal splicing region ...DNA polymerase II intein domain IV / DNA polymerase II intein Domain IV / LAGLIDADG-like domain / Intein splicing domain / Intein / Intein DOD homing endonuclease / Intein DOD-type homing endonuclease domain profile. / DNA Polymerase; Chain A, domain 1 / DNA Polymerase, chain B, domain 1 / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Homing endonuclease, LAGLIDADG / B family DNA polymerase, finger domain / Palm domain of DNA polymerase / B family DNA polymerase, palm domain / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / Hint domain superfamily / Homing endonuclease / DNA polymerase family B, thumb 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-directed DNA polymerase, family B, multifunctional 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-HHZ / : / NITRATE ION / DNA / DNA (> 10) / DNA polymerase
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.997 Å
AuthorsKropp, H.M. / Diederichs, K. / Marx, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
Germany
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2019
Title: The Structure of an Archaeal B-Family DNA Polymerase in Complex with a Chemically Modified Nucleotide.
Authors: Kropp, H.M. / Diederichs, K. / Marx, A.
History
DepositionDec 6, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.journal_abbrev / _citation.title ..._citation.journal_abbrev / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2Apr 10, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.3Aug 14, 2019Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rrim_I_all / _reflns_shell.pdbx_Rrim_I_all
Revision 1.4Jan 24, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type
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.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.value / _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.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase,DNA polymerase,DNA polymerase
T: DNA (5'-D(P*AP*AP*CP*TP*GP*TP*GP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')
P: DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*CP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,99517
Polymers98,5923
Non-polymers1,40314
Water4,990277
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8170 Å2
ΔGint-25 kcal/mol
Surface area36350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.940, 146.424, 71.477
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA polymerase,DNA polymerase,DNA polymerase


Mass: 90060.461 Da / Num. of mol.: 1 / Mutation: D141A, E143A,D141A, E143A,D141A, E143A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea)
Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Gene: pol, TK0001 / Production host: Escherichia coli (E. coli)
References: UniProt: P77933, DNA-directed DNA polymerase, Hydrolases; Acting on ester bonds

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DNA chain , 2 types, 2 molecules TP

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


Mass: 4930.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*CP*AP*C)-3')


Mass: 3601.372 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 7 types, 291 molecules

#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-HHZ / [[(2~{R},3~{S},5~{R})-5-[4-azanyl-5-[3-[2-(2-hydroxyethyloxy)ethanoylamino]prop-1-ynyl]pyrrolo[2,3-d]pyrimidin-7-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate


Mass: 645.345 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H26N5O15P3 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#9: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 277 / 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: 2.86 Å3/Da / Density % sol: 57.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.09M sodium nitrate, 0.09 sodium phosphate dibasic, 0.09M ammonium sulfate, 0.1 M Tris base, 0.1 M BICINE, 12.5 % MPD, 12.5 % PEG 1000, 12.5 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.997→48.808 Å / Num. obs: 138630 / % possible obs: 93.3 % / Redundancy: 3.38 % / Rrim(I) all: 0.189 / Net I/σ(I): 5.6
Reflection shellResolution: 1.997→2.007 Å / Redundancy: 2.43 % / Mean I/σ(I) obs: 0.35 / Num. unique obs: 16466 / Rrim(I) all: 2.542 / % possible all: 68.5

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Processing

Software
NameVersionClassification
PHENIX(dev_3283: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OMF

5omf


Resolution: 1.997→46.219 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.87 / Phase error: 29.58
RfactorNum. reflection% reflection
Rfree0.2311 6636 4.8 %
Rwork0.2023 --
obs0.2037 138318 93.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.997→46.219 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6221 569 85 277 7152
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047121
X-RAY DIFFRACTIONf_angle_d0.7019718
X-RAY DIFFRACTIONf_dihedral_angle_d20.1724213
X-RAY DIFFRACTIONf_chiral_restr0.0451033
X-RAY DIFFRACTIONf_plane_restr0.0041160
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9966-2.01930.54391330.48622729X-RAY DIFFRACTION59
2.0193-2.0430.49981620.47142965X-RAY DIFFRACTION63
2.043-2.06790.42791630.43043257X-RAY DIFFRACTION69
2.0679-2.09410.38841660.39923415X-RAY DIFFRACTION72
2.0941-2.12170.38711770.40343661X-RAY DIFFRACTION77
2.1217-2.15070.42771960.36583819X-RAY DIFFRACTION82
2.1507-2.18150.38371980.35334126X-RAY DIFFRACTION87
2.1815-2.2140.35882020.3294426X-RAY DIFFRACTION94
2.214-2.24860.31182540.32184715X-RAY DIFFRACTION100
2.2486-2.28550.32042510.31324636X-RAY DIFFRACTION100
2.2855-2.32490.29782140.29824772X-RAY DIFFRACTION100
2.3249-2.36720.28812260.28324684X-RAY DIFFRACTION100
2.3672-2.41270.30882100.27924734X-RAY DIFFRACTION100
2.4127-2.46190.27152340.27454724X-RAY DIFFRACTION100
2.4619-2.51550.27512760.25954618X-RAY DIFFRACTION100
2.5155-2.5740.29832430.26394761X-RAY DIFFRACTION100
2.574-2.63830.28672300.25324699X-RAY DIFFRACTION100
2.6383-2.70970.26912550.24154663X-RAY DIFFRACTION100
2.7097-2.78940.25292170.22744711X-RAY DIFFRACTION99
2.7894-2.87940.27192400.21954662X-RAY DIFFRACTION99
2.8794-2.98230.2512470.20044681X-RAY DIFFRACTION100
2.9823-3.10170.22322160.20544743X-RAY DIFFRACTION100
3.1017-3.24280.23742460.19734702X-RAY DIFFRACTION100
3.2428-3.41370.2242380.17534672X-RAY DIFFRACTION100
3.4137-3.62750.18682590.16564691X-RAY DIFFRACTION100
3.6275-3.90750.1992340.16114695X-RAY DIFFRACTION99
3.9075-4.30050.17262270.13784649X-RAY DIFFRACTION99
4.3005-4.92210.15012250.12864733X-RAY DIFFRACTION100
4.9221-6.1990.20952400.15284687X-RAY DIFFRACTION100
6.199-46.23090.18152570.16724652X-RAY DIFFRACTION99
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)
11.9497-0.1303-1.28050.57440.33122.23010.04860.01020.1848-0.01840.0306-0.0202-0.03770.0318-0.10450.2727-0.0258-0.04420.30550.0370.2985-16.000439.7498-7.1635
23.7485-0.3041-0.481.330.41361.9324-0.00390.2777-0.3348-0.11950.00420.080.1353-0.09140.00190.326-0.0178-0.01540.35150.05330.2993-10.669529.4402-25.5087
31.22840.4920.3491.11010.36561.05930.02770.02540.0108-0.0142-0.03270.06120.0506-0.0240.0050.27370.02110.00370.29530.02830.2747-43.180523.3811-14.189
42.8856-1.03390.19270.965-0.07631.08610.07690.2479-0.1533-0.145-0.0395-0.20210.14630.238-0.03230.3712-0.02540.04320.3736-0.02250.47-28.17573.4826-30.6501
57.12992.1735-0.35776.40730.90168.93190.0120.6165-1.264-0.85540.1089-1.50450.35061.7654-0.07390.48830.07450.05080.6968-0.0170.688-27.38719.1157-11.4616
63.3863-0.4647-0.54352.38631.82531.5830.1171-0.0144-0.5441-0.0642-0.0851-0.16360.08270.2537-0.04220.38260.00020.00090.41310.10730.4845-29.9579-3.2421-15.2025
71.8817-2.46030.81176.1661-2.06581.2485-0.0566-0.2526-0.22120.05870.10350.2940.124-0.1038-0.03980.44490.00550.03420.4561-0.04530.4516-30.7323-0.9273-15.8983
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 214 )
2X-RAY DIFFRACTION2chain 'A' and (resid 215 through 337 )
3X-RAY DIFFRACTION3chain 'A' and (resid 338 through 552 )
4X-RAY DIFFRACTION4chain 'A' and (resid 553 through 756 )
5X-RAY DIFFRACTION5chain 'T' and (resid 1 through 5 )
6X-RAY DIFFRACTION6chain 'T' and (resid 6 through 16 )
7X-RAY DIFFRACTION7chain 'P' and (resid 1 through 12 )

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