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- PDB-7k5t: Bst DNA polymerase I time-resolved structure, 25.5 hr post dATP a... -

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Basic information

Entry
Database: PDB / ID: 7k5t
TitleBst DNA polymerase I time-resolved structure, 25.5 hr post dATP and dCTP addition
Components
  • DNA (5'-D(P*CP*GP*AP*TP*CP*AP*CP*GP*TP*A)-3')
  • DNA (5'-D(P*CP*GP*TP*AP*CP*GP*TP*GP*AP*TP*CP*GP*C)-3')
  • DNA polymerase I
KeywordsTRANSFERASE/DNA / DNA polymerase / TRANSFERASE / TRANSFERASE-DNA complex
Function / homology
Function and homology information


3'-5' exonuclease activity / DNA-templated DNA replication / double-strand break repair / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding / metal ion binding
Similarity search - Function
: / DNA polymerase I, ribonuclease H-like domain / DNA polymerase 1 / Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / 3'-5' exonuclease / 3'-5' exonuclease domain / DNA polymerase A / DNA polymerase family A / DNA-directed DNA polymerase, family A, conserved site ...: / DNA polymerase I, ribonuclease H-like domain / DNA polymerase 1 / Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / 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 / 5' to 3' exonuclease, C-terminal subdomain / Ribonuclease H-like superfamily/Ribonuclease H / DNA polymerase; domain 1 / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase I
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsChim, N. / Meza, R.A. / Trinh, A.M. / Chaput, J.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE 2001434 United States
CitationJournal: Nat Commun / Year: 2021
Title: Following replicative DNA synthesis by time-resolved X-ray crystallography.
Authors: Chim, N. / Meza, R.A. / Trinh, A.M. / Yang, K. / Chaput, J.C.
History
DepositionSep 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1May 19, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 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(P*CP*GP*AP*TP*CP*AP*CP*GP*TP*A)-3')
T: DNA (5'-D(P*CP*GP*TP*AP*CP*GP*TP*GP*AP*TP*CP*GP*C)-3')
A: DNA polymerase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,2717
Polymers74,5153
Non-polymers7554
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-55 kcal/mol
Surface area28010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.631, 93.589, 105.471
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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DNA chain , 2 types, 2 molecules PT

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


Mass: 4923.204 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 / Bst 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, 124 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-DCP / 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O13P3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.87 Å3/Da / Density % sol: 57.13 %
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 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→46.79 Å / Num. obs: 38768 / % possible obs: 99.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 40.57 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06221 / Rpim(I) all: 0.02661 / Rrim(I) all: 0.06778 / Net I/σ(I): 19.23
Reflection shellResolution: 2.3→2.382 Å / Rmerge(I) obs: 0.4801 / Num. unique obs: 3819 / CC1/2: 0.932 / Rpim(I) all: 0.198 / Rrim(I) all: 0.5198

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
autoXDSdata reduction
autoXDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DSY

6dsy


Resolution: 2.3→46.79 Å / SU ML: 0.286 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.7364 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2367 1790 4.62 %
Rwork0.191 36923 -
obs0.1932 38713 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.51 Å2
Refinement stepCycle: LAST / Resolution: 2.3→46.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4641 470 26 120 5257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00785274
X-RAY DIFFRACTIONf_angle_d0.88117227
X-RAY DIFFRACTIONf_chiral_restr0.0495813
X-RAY DIFFRACTIONf_plane_restr0.0054855
X-RAY DIFFRACTIONf_dihedral_angle_d10.33543136
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.31991140.24392837X-RAY DIFFRACTION100
2.36-2.430.28991450.23092782X-RAY DIFFRACTION99.97
2.43-2.510.29531420.22122813X-RAY DIFFRACTION99.9
2.51-2.60.26861370.21322794X-RAY DIFFRACTION99.93
2.6-2.70.30141270.21522824X-RAY DIFFRACTION99.97
2.7-2.830.27231480.212798X-RAY DIFFRACTION99.9
2.83-2.980.26531320.22162831X-RAY DIFFRACTION100
2.98-3.160.30341450.21932797X-RAY DIFFRACTION99.93
3.16-3.410.25151300.20472856X-RAY DIFFRACTION99.97
3.41-3.750.25241420.18682816X-RAY DIFFRACTION98.73
3.75-4.290.18131400.16262862X-RAY DIFFRACTION99.8
4.29-5.410.18611470.15432885X-RAY DIFFRACTION99.9
5.41-46.790.22441410.18883028X-RAY DIFFRACTION99.62
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)
11.80228044835-0.0915969621673-1.39914660113.858288613782.974050251434.07618617690.5788527598561.06350793252-0.324193806174-0.148851289828-1.37397334080.03049661191490.64218177273-1.562303000660.7828039318331.105052022170.0750430933657-0.01131975837311.09277970832-0.2397479767230.84099396965728.954242266728.391943933133.0734525706
23.24404158450.001825670928060.891837640742.56761157791-0.4841109450722.569378383770.2489046372340.255220566899-0.7873110399170.697320098498-0.5495413524750.9559633275561.7956717024-0.6026020287120.4343637512391.310307970450.05558390962910.0670636250190.928242914538-0.21361550621.0012718886828.124435632627.792039824132.9180015369
32.28393297220.77196531986-0.02523647290332.155097859420.1492414043141.19753526196-0.06648554969250.248713275136-0.0594022632273-0.431005051860.0837311168296-0.0203181215820.04709786886850.0331920215338-0.009907680487320.356363429941-0.005949797777610.009338787532970.28923578724-0.0169288859430.2510336903111.04971489727.43921062325.18800202229
40.8001456532490.05028637302490.202756235490.8851590883440.01661492661271.29926086552-0.03755551105950.0153348464132-0.006422565962380.00822839491095-0.0403911621825-0.1077180710760.001102931963540.1433760183510.06515566538520.2987569297430.01334888628710.01519949135520.259291441610.01680733010510.29791424849317.384235560236.129935272219.8063302301
50.6511266836430.02106004032861.23649294630.9735392279740.06543003459962.63299336230.140443874110.00237768833922-0.006414211801790.3433256788750.0176163617275-0.1517316483030.5658558547720.0899661019035-0.1321380204050.6249473663210.0327897739242-0.02774288131650.469650213893-0.01647636301640.44703556128535.643473627837.155069082240.1153434314
61.366953973740.515696665146-0.5225265340922.36148513027-0.01692481874150.6368794734750.0951843485011-0.1314506108040.1527213744370.4423624957260.0982208728065-0.0566342429431-0.2350266223820.065722047739-0.2370089883260.4419043778880.03352085404690.04039916628550.3458831005910.006507881493950.39091579114120.194394197545.485694015426.2187697974
70.5903048369240.400333080175-0.1688006738341.214889773490.03308039392971.935406214670.0239889038711-0.135986995988-0.05671935438860.25686887606-0.0268510776805-0.1678475767420.0348870286810.0471295063923-0.01273728660190.3425961795610.00501632574177-0.04914962483810.308244048026-0.004676465787590.343885866516.7034766060147.958893718746.1152416687
80.7862820690940.463325753887-0.3045021411061.45588477503-0.3283680064861.154755642760.100834042206-0.0532234547544-0.006416992931340.295103478261-0.0506572352571-0.0165143915204-0.146760759665-0.0708565901678-0.02661027374380.3103374486060.00516564197999-0.01494325740390.289004582243-0.01336060249850.3188687855934.5813045967143.254316726633.1636185234
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'P' and (resid 2 through 11 )
2X-RAY DIFFRACTION2chain 'T' and (resid 3 through 15 )
3X-RAY DIFFRACTION3chain 'A' and (resid 300 through 439 )
4X-RAY DIFFRACTION4chain 'A' and (resid 440 through 522 )
5X-RAY DIFFRACTION5chain 'A' and (resid 523 through 604 )
6X-RAY DIFFRACTION6chain 'A' and (resid 605 through 646 )
7X-RAY DIFFRACTION7chain 'A' and (resid 647 through 728 )
8X-RAY DIFFRACTION8chain 'A' and (resid 729 through 876 )

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