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- PDB-7k5o: Bst DNA polymerase I time-resolved structure, 1 min post dATP addition -

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Basic information

Entry
Database: PDB / ID: 7k5o
TitleBst DNA polymerase I time-resolved structure, 1 min post dATP addition
Components
  • DNA (5'-D(*GP*CP*GP*AP*TP*CP*AP*CP*GP*T)-3')
  • DNA (5'-D(P*TP*AP*CP*GP*TP*GP*AP*TP*CP*GP*CP*A)-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: 2.16 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(*GP*CP*GP*AP*TP*CP*AP*CP*GP*T)-3')
T: DNA (5'-D(P*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)74,6828
Polymers74,2023
Non-polymers4805
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-82 kcal/mol
Surface area27590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.990, 93.050, 104.819
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(*GP*CP*GP*AP*TP*CP*AP*CP*GP*T)-3')


Mass: 3045.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*TP*AP*CP*GP*TP*GP*AP*TP*CP*GP*CP*A)-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.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.86 Å3/Da / Density % sol: 56.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 50% saturated 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: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.16→44.89 Å / Num. obs: 46274 / % possible obs: 99.9 % / Redundancy: 7 % / Biso Wilson estimate: 34.22 Å2 / CC1/2: 0.997 / Net I/σ(I): 12.5
Reflection shellResolution: 2.16→2.237 Å / Num. unique obs: 4541 / CC1/2: 0.776

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Processing

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

6dsy


Resolution: 2.16→44.89 Å / SU ML: 0.2479 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.9932 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2268 2008 4.34 %
Rwork0.1864 44253 -
obs0.1881 46261 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.9 Å2
Refinement stepCycle: LAST / Resolution: 2.16→44.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4636 448 25 206 5315
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00795258
X-RAY DIFFRACTIONf_angle_d0.89547206
X-RAY DIFFRACTIONf_chiral_restr0.0519807
X-RAY DIFFRACTIONf_plane_restr0.0052858
X-RAY DIFFRACTIONf_dihedral_angle_d9.02634304
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.16-2.210.31961340.27913096X-RAY DIFFRACTION99.97
2.21-2.270.34011590.28253106X-RAY DIFFRACTION99.66
2.27-2.340.27271240.23563120X-RAY DIFFRACTION99.97
2.34-2.420.25021530.22473118X-RAY DIFFRACTION99.91
2.42-2.50.27651400.20743155X-RAY DIFFRACTION99.97
2.5-2.60.2621340.20093116X-RAY DIFFRACTION99.97
2.6-2.720.2641590.20383129X-RAY DIFFRACTION100
2.72-2.860.25341340.20173145X-RAY DIFFRACTION99.97
2.86-3.040.27321380.20133158X-RAY DIFFRACTION100
3.04-3.280.25351430.19363160X-RAY DIFFRACTION99.94
3.28-3.610.22711460.17753184X-RAY DIFFRACTION99.94
3.61-4.130.18951450.15583191X-RAY DIFFRACTION99.82
4.13-5.20.18521430.14943222X-RAY DIFFRACTION99.88
5.2-44.890.17881560.17613353X-RAY DIFFRACTION99.86
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)
17.348541963722.30572266540.06374640114576.811402018821.607969463268.947018618150.1236930086390.492419619186-0.1374321533340.827228609201-0.1913543177470.639819932791.36203971549-1.151499096770.04773736254250.7551255330690.0586727595925-0.06759787203660.798847609943-0.08488871642870.49346107389526.665733061930.67926462834.4460147923
25.32860439078-2.675866260061.811398939289.01744021389-2.049903665355.402118555920.07031397557420.0390907680802-1.044335306461.3494707231-0.1298413019930.4897300784791.78597674864-0.4767469638080.147316490551.125741446650.07362387577470.02834298762590.722644325314-0.1364476207490.59043816274827.23499050928.764399568633.281342496
33.089670908120.828465841842-0.3980812446163.53565299553-0.2030807373582.00200420362-0.02634384110580.275279810553-0.0749564661312-0.3939653926850.0782244673961-0.0697838652320.03978472515110.0421189875245-0.04516203983840.225642734116-0.01061099772570.009899459982130.202313589819-0.02038022248250.17208742643111.019661630927.24075838525.10622989878
41.016413006430.165804293323-0.176514220861.29323980444-0.0683773784821.33088944419-0.0319784873552-0.0129172271153-0.05208793076520.13889606743-0.011358786514-0.158013590513-0.0223277923470.2151807336870.01326777362250.2140012868490.01001556599680.01119127778650.1936372109370.01801413213070.18837189536717.161236980135.88702486419.392994491
51.50409819845-0.4864524011763.346381783131.96539111918-0.5630464613357.546312298310.192735140331-0.0619274074422-0.01587989432990.464975502502-0.0172697155567-0.2124714898810.8003328030390.312807496726-0.1353907893890.5061769365280.0421595629706-0.01944232240010.396899014142-0.01062247094650.35365714422835.735063882436.840049895839.8312660876
61.94841544402-0.197434458673-1.557028853771.910294964450.3537768151351.94743119648-0.059001125539-0.1605578551230.05457012449060.006709463358320.0617123803729-0.2011325858330.1092191153490.205549658693-0.01413268664930.2237881234410.00466637744461-0.03902473827450.2315842695210.02098471563670.20426900770812.490036019446.989419885630.5370815459
76.71179006326-1.374863361362.147585980226.37766488158-2.35021102945.882281523180.400961103081-0.0485487939011-0.477965639681-0.0283567603936-0.196913176099-0.2400189984380.3143410957120.273736644018-0.1293840740530.3201599567660.00681824749503-0.1320328229750.282522243545-0.007701014679770.3147695606649.7768393694846.390133988551.4143552249
81.209385907210.811957670763-0.6510589293572.3493418746-1.052848057551.407730732720.0802726956553-0.10487071186-0.02488718902660.209935882467-0.0667247058833-0.123425780599-0.0966707968393-0.0265031093833-0.006785424686360.27316218893-0.01037561757630.003167604746170.22940271186-0.02074408563670.2375253262984.6789678794942.970820957432.9371403297
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'P' and (resid 1 through 10 )
2X-RAY DIFFRACTION2chain 'T' and (resid 5 through 16 )
3X-RAY DIFFRACTION3chain 'A' and (resid 300 through 439 )
4X-RAY DIFFRACTION4chain 'A' and (resid 440 through 521 )
5X-RAY DIFFRACTION5chain 'A' and (resid 522 through 604 )
6X-RAY DIFFRACTION6chain 'A' and (resid 605 through 676 )
7X-RAY DIFFRACTION7chain 'A' and (resid 677 through 728 )
8X-RAY DIFFRACTION8chain 'A' and (resid 729 through 876 )

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