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- PDB-6dsx: Bst DNA polymerase I post-chemistry (n+1 with dATP soak) structure -

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Basic information

Entry
Database: PDB / ID: 6dsx
TitleBst DNA polymerase I post-chemistry (n+1 with dATP soak) structure
Components
  • DNA (5'-D(*GP*CP*GP*AP*TP*CP*AP*CP*GP*TP*A)-3')
  • DNA (5'-D(*GP*TP*AP*CP*GP*TP*GP*AP*TP*CP*GP*CP*A)-3')
  • DNA polymerase I
KeywordsTRANSFERASE/DNA / DNA synthesis / TRANSFERASE / TRANSFERASE-DNA complex
Function / homology
Function and homology information


double-strand break repair via alternative nonhomologous end joining / 3'-5' exonuclease activity / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding / metal ion binding
Similarity search - Function
Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / DNA polymerase 1 / Alpha-Beta Plaits - #370 / 3'-5' exonuclease / 3'-5' exonuclease domain / DNA polymerase A / DNA polymerase family A / DNA-directed DNA polymerase, family A, conserved site / DNA polymerase family A signature. ...Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / DNA polymerase 1 / Alpha-Beta Plaits - #370 / 3'-5' exonuclease / 3'-5' exonuclease domain / 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 / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Alpha-Beta Plaits / DNA/RNA polymerase superfamily / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA polymerase I
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsChim, N. / Jackson, L.N. / Chaput, J.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB: 1607111 United States
CitationJournal: Elife / Year: 2018
Title: Crystal structures of DNA polymerase I capture novel intermediates in the DNA synthesis pathway.
Authors: Chim, N. / Jackson, L.N. / Trinh, A.M. / Chaput, J.C.
History
DepositionJun 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)74,37712
Polymers73,5843
Non-polymers7939
Water4,990277
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6110 Å2
ΔGint-123 kcal/mol
Surface area28180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.116, 93.576, 105.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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DNA chain , 2 types, 2 molecules PT

#1: DNA chain DNA (5'-D(*GP*CP*GP*AP*TP*CP*AP*CP*GP*TP*A)-3')


Mass: 3358.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*GP*TP*AP*CP*GP*TP*GP*AP*TP*CP*GP*CP*A)-3')


Mass: 3991.610 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Protein , 1 types, 1 molecules A

#3: Protein DNA polymerase I


Mass: 66233.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: polA / Production host: Escherichia coli (E. coli) / References: UniProt: E1C9K5, DNA-directed DNA polymerase

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Non-polymers , 3 types, 286 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / 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: 2.91 Å3/Da / Density % sol: 57.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 50% ammonium sulfate, 0.1M MES, 2% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→46.79 Å / Num. obs: 59689 / % possible obs: 99.92 % / Redundancy: 6.8 % / CC1/2: 0.993 / Rmerge(I) obs: 0.132 / Net I/σ(I): 17.03
Reflection shellResolution: 1.99→2.061 Å / Rmerge(I) obs: 0.719 / Num. unique obs: 5857 / CC1/2: 0.795

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
autoXDSdata reduction
autoXDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1L3U

1l3u


Resolution: 1.99→46.788 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2197 1992 3.34 %
Rwork0.1845 --
obs0.1857 59677 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.99→46.788 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4654 488 41 277 5460
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085313
X-RAY DIFFRACTIONf_angle_d0.8347289
X-RAY DIFFRACTIONf_dihedral_angle_d9.2063150
X-RAY DIFFRACTIONf_chiral_restr0.053814
X-RAY DIFFRACTIONf_plane_restr0.005857
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.03980.29981380.24544064X-RAY DIFFRACTION100
2.0398-2.09490.29481500.21554050X-RAY DIFFRACTION100
2.0949-2.15660.23741420.20234064X-RAY DIFFRACTION100
2.1566-2.22620.21811290.18264073X-RAY DIFFRACTION100
2.2262-2.30580.23361550.18074075X-RAY DIFFRACTION100
2.3058-2.39810.23041340.18464102X-RAY DIFFRACTION100
2.3981-2.50720.22331520.18994075X-RAY DIFFRACTION100
2.5072-2.63940.23761250.19444124X-RAY DIFFRACTION100
2.6394-2.80470.30161500.20444092X-RAY DIFFRACTION100
2.8047-3.02120.26411430.21064099X-RAY DIFFRACTION100
3.0212-3.32520.21481410.19774149X-RAY DIFFRACTION100
3.3252-3.80620.21421430.17034168X-RAY DIFFRACTION100
3.8062-4.79460.15881420.15224181X-RAY DIFFRACTION100
4.7946-46.80090.20851480.18414369X-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)
15.8198-1.7776-2.59689.44616.18324.7280.24630.869-0.43510.6808-0.66380.74670.7123-0.35160.39370.77450.0804-0.09760.6545-0.08860.453727.523730.005933.4229
28.5424-0.17732.1236.6328-1.30641.327-0.1848-0.1973-0.52221.23350.23770.1351.6276-0.02930.12331.10270.1241-0.06090.536-0.09180.4228.156128.328732.8216
34.17281.40871.07373.1381.34544.0097-0.18290.5155-0.2592-0.65550.1931-0.06070.0893-0.0543-0.02170.3025-0.02710.05070.192-0.00370.171111.19725.8507-1.0911
42.41270.9645-0.40772.3236-0.02582.0431-0.03290.1255-0.0716-0.14920.02340.00310.1141-0.001-0.00340.1266-0.008-0.01150.1602-0.01170.13629.224226.16858.5246
51.08980.02450.47261.5621-0.38852.2481-0.10460.15080.2910.1993-0.0603-0.2537-0.22750.47490.20070.22050.0056-0.01630.2141-0.01660.205524.00643.860425.3271
61.2038-1.16122.6312.4528-1.27576.6240.01550.01110.04870.66250.1135-0.29990.46460.3804-0.04140.52380.0169-0.07740.358-0.0030.335135.510937.198940.1038
71.706-0.0898-1.16841.34510.23771.7095-0.0081-0.14890.04910.1006-0.0064-0.1727-0.10430.1930.02560.2239-0.0141-0.05470.22150.02060.202112.566747.356530.745
86.685-0.80242.06494.9576-1.34565.14790.2049-0.072-0.42560.3985-0.1304-0.26960.18180.0583-0.0460.2592-0.0018-0.05870.243-0.0120.20798.341744.658253.2261
91.21770.5658-0.32932.1041-0.78471.60410.0836-0.05110.03140.1592-0.05450.0392-0.0942-0.1077-0.01780.1515-0.0147-0.00120.1781-0.02480.16484.570543.649630.2753
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'P' and (resid 0 through 10 )
2X-RAY DIFFRACTION2chain 'T' and (resid 4 through 16 )
3X-RAY DIFFRACTION3chain 'A' and (resid 297 through 347 )
4X-RAY DIFFRACTION4chain 'A' and (resid 348 through 467 )
5X-RAY DIFFRACTION5chain 'A' and (resid 468 through 522 )
6X-RAY DIFFRACTION6chain 'A' and (resid 523 through 604 )
7X-RAY DIFFRACTION7chain 'A' and (resid 605 through 676 )
8X-RAY DIFFRACTION8chain 'A' and (resid 677 through 743 )
9X-RAY DIFFRACTION9chain 'A' and (resid 744 through 876 )

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