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- PDB-7k5s: Bst DNA polymerase I time-resolved structure, 4 hr post dATP and ... -

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Basic information

Entry
Database: PDB / ID: 7k5s
TitleBst DNA polymerase I time-resolved structure, 4 hr post dATP and dCTP addition
Components
  • DNA (5'-D(*CP*GP*AP*TP*CP*AP*CP*GP*TP*A)-3')
  • DNA (5'-D(P*AP*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
DNA / DNA (> 10) / DNA polymerase I
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 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(*CP*GP*AP*TP*CP*AP*CP*GP*TP*A)-3')
T: DNA (5'-D(P*AP*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)74,8046
Polymers74,5153
Non-polymers2883
Water10,503583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5770 Å2
ΔGint-53 kcal/mol
Surface area27750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.622, 93.416, 105.870
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

#1: DNA chain DNA (5'-D(*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*AP*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)
#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
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 583 / Source method: isolated from a natural source / Formula: H2O
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: 57.21 %
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: Mar 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.67→46.05 Å / Num. obs: 99196 / % possible obs: 98.09 % / Redundancy: 6.5 % / Biso Wilson estimate: 24.69 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0549 / Rpim(I) all: 0.0235 / Rrim(I) all: 0.05983 / Net I/σ(I): 18.14
Reflection shellResolution: 1.67→1.73 Å / Rmerge(I) obs: 0.8071 / Num. unique obs: 9747 / CC1/2: 0.849 / Rpim(I) all: 0.3296 / Rrim(I) all: 0.8728

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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: 1.67→46.05 Å / SU ML: 0.1712 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.5838 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2096 1978 2.01 %
Rwork0.1868 96202 -
obs0.1872 98180 98.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.15 Å2
Refinement stepCycle: LAST / Resolution: 1.67→46.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4641 488 10 583 5722
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00615277
X-RAY DIFFRACTIONf_angle_d0.81537236
X-RAY DIFFRACTIONf_chiral_restr0.0504813
X-RAY DIFFRACTIONf_plane_restr0.005855
X-RAY DIFFRACTIONf_dihedral_angle_d9.95763145
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.67-1.710.30531460.25686801X-RAY DIFFRACTION98.61
1.71-1.760.23371370.22066832X-RAY DIFFRACTION98.42
1.76-1.810.22371510.21416838X-RAY DIFFRACTION98.95
1.81-1.870.26261300.21886852X-RAY DIFFRACTION98.6
1.87-1.940.45681330.3566281X-RAY DIFFRACTION90.52
1.94-2.010.21851340.19866914X-RAY DIFFRACTION99.06
2.01-2.10.20391360.18016889X-RAY DIFFRACTION99.15
2.1-2.210.20811430.18116897X-RAY DIFFRACTION99.09
2.21-2.350.27181420.2336545X-RAY DIFFRACTION93.59
2.35-2.540.23031420.18796947X-RAY DIFFRACTION99.38
2.54-2.790.20371370.19367004X-RAY DIFFRACTION99.54
2.79-3.190.21081460.18897009X-RAY DIFFRACTION99.55
3.19-4.020.18891470.16027068X-RAY DIFFRACTION99.3
4.02-46.050.161540.15887325X-RAY DIFFRACTION99.47
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)
12.97335393359-0.637184592025-0.1333725580133.28235906176-0.04049787532151.952077412510.09270510435610.867394672225-0.7087925808790.231217141261-0.336653727721-0.1650436911440.7664379972320.3890951835350.1601354166550.5423505521060.159506646094-0.02988619634420.513374888771-0.1397882746410.51822674490426.354065008830.998184041534.4824348363
24.62906658662-0.376933728826-0.1813350571770.3913598816480.7020377889431.29268014133-0.347622361738-0.485925492368-0.422365724990.5059267604510.339493251549-0.329046473271.379582935820.6009057912980.1791725096870.6266018922080.257152207165-0.01940219979650.428097444875-0.03111449620130.4817297475425.064797752328.735828727936.0372445146
31.44691482670.677154011334-0.3205096096691.83075121572-0.1591180502181.01391755417-0.05811245607760.149793065249-0.109279246029-0.2550146732920.043454822531-0.09775430479680.08179267611410.008483734033110.00904829762340.218353971888-0.0139501851270.01460418165950.202403988791-0.01107391741940.185064327699.6873560470526.11202382945.76207058846
40.2848307095540.0358137759665-0.1590324512221.38723856347-0.6267353672741.40955335234-0.09862505550830.05158583479270.2540359322650.0968119556277-0.0538238126011-0.172177728652-0.1033462398820.3995734930450.176340983250.2120818870580.01580246482010.02075357178130.241965155641-0.0355096197880.18261706818724.340016426543.554424742325.4713257744
50.835437506717-0.6686018763892.214319994871.38415422417-0.7224799599934.21933982165-0.0168600156352-0.0882094285048-0.01213070065240.5480114605430.116290184966-0.172124717280.3399596007820.185344540369-0.07389514116840.4985703459560.0930750332993-0.04155514759130.3972270788630.02418822852140.3041244778435.388442248636.882409767340.2348760863
60.885107766283-0.0916675258788-0.7156661754240.829649707455-0.08427524008191.071118057550.0145621260452-0.04321121863440.0955153539070.041077918403-0.0145438765386-0.0868922495024-0.06880459360650.07508003288660.003242878397510.174994156263-0.00969167970596-0.01498660015630.1758091190610.006754756239460.18482143059612.680181805346.942784774130.7345561918
72.686378461610.380308076931.075304287432.635513769549.4797628198E-52.011925437240.00348967088784-0.139144259709-0.1442082212360.3533581576070.00675800344089-0.1974436765450.0961609351180.0321628465638-0.018951866490.2506767214320.0154224190287-0.0273247840570.223376236614-0.003803545508510.1996811562418.2814959552144.200753630853.5796968442
80.7821743542580.429574331153-0.3462502299191.24847419829-0.3012691236770.8643175926210.0662307262692-0.01649444681050.01650498674370.0753363683374-0.04228532248050.02439530785670.0123688148528-0.0276579843897-0.03774106072640.162720845001-0.00574504025728-0.001226736958790.174574140869-0.007792049930160.1745057650864.717025604643.283985176330.3611009967
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'P' and (resid 2 through 11 )
2X-RAY DIFFRACTION2chain 'T' and (resid 2 through 15 )
3X-RAY DIFFRACTION3chain 'A' and (resid 300 through 467 )
4X-RAY DIFFRACTION4chain 'A' and (resid 468 through 522 )
5X-RAY DIFFRACTION5chain 'A' and (resid 523 through 604 )
6X-RAY DIFFRACTION6chain 'A' and (resid 605 through 676 )
7X-RAY DIFFRACTION7chain 'A' and (resid 677 through 743 )
8X-RAY DIFFRACTION8chain 'A' and (resid 744 through 876 )

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