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- PDB-7k5q: Bst DNA polymerase I time-resolved structure, 8 min post dATP addition -

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Basic information

Entry
Database: PDB / ID: 7k5q
TitleBst DNA polymerase I time-resolved structure, 8 min post dATP addition
Components
  • DNA (5'-D(P*G*CP*GP*AP*TP*CP*AP*CP*GP*T)-3')
  • DNA (5'-D(P*GP*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


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
DNA polymerase 1 / 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 superfamily ...DNA polymerase 1 / 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 superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
2'-DEOXYADENOSINE 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 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*G*CP*GP*AP*TP*CP*AP*CP*GP*T)-3')
T: DNA (5'-D(P*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)74,9827
Polymers74,2023
Non-polymers7794
Water7,909439
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-55 kcal/mol
Surface area28270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.200, 93.988, 105.724
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*G*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*GP*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)

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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, 443 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 491.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 439 / 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: 2.95 Å3/Da / Density % sol: 58.35 %
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: Sep 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→39.92 Å / Num. obs: 59144 / % possible obs: 95.71 % / Redundancy: 4.7 % / Biso Wilson estimate: 27.25 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.06529 / Rpim(I) all: 0.0342 / Rrim(I) all: 0.07403 / Net I/σ(I): 14.87
Reflection shellResolution: 2→2.071 Å / Rmerge(I) obs: 0.2992 / Num. unique obs: 5882 / CC1/2: 0.951 / Rpim(I) all: 0.1495 / Rrim(I) all: 0.3353

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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→39.92 Å / SU ML: 0.2113 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.1 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2464 1504 2.62 %
Rwork0.1936 55944 -
obs0.1949 57448 95.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.96 Å2
Refinement stepCycle: LAST / Resolution: 2→39.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4628 473 36 439 5576
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00775275
X-RAY DIFFRACTIONf_angle_d0.86617231
X-RAY DIFFRACTIONf_chiral_restr0.0522812
X-RAY DIFFRACTIONf_plane_restr0.0053854
X-RAY DIFFRACTIONf_dihedral_angle_d10.08373133
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.060.24551410.19875233X-RAY DIFFRACTION99.94
2.06-2.140.21621380.19615236X-RAY DIFFRACTION99.78
2.14-2.220.3181240.25854990X-RAY DIFFRACTION94.58
2.22-2.330.47561010.35933562X-RAY DIFFRACTION68.07
2.33-2.450.28171390.21595257X-RAY DIFFRACTION99.8
2.45-2.60.26191480.20345265X-RAY DIFFRACTION99.52
2.6-2.80.27991380.20255238X-RAY DIFFRACTION99.43
2.8-3.080.2321430.19915283X-RAY DIFFRACTION99.43
3.08-3.530.23251500.18215275X-RAY DIFFRACTION98.69
3.53-4.450.23451350.16495230X-RAY DIFFRACTION97.14
4.45-39.920.19421470.16675375X-RAY DIFFRACTION96.35
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)
12.20202486842-1.37003663577-1.825473545514.547849016674.660581013154.92851150350.5329835655420.439953986301-0.3578954038160.585343062616-1.28776153720.5843429207611.08169319675-2.260540124430.6571729615210.8806594074330.07514208843370.01858146836470.938659945189-0.1867276849920.53078521806629.404919388428.046032885633.1804077899
25.208057396160.3760713025270.4322916929645.892967546852.399728935796.814166044260.4339623247550.725555861553-1.222107364890.469477858973-0.818801041050.8320984560392.1619821901-0.3704791950040.4391851272141.099470993320.149267170456-0.1160312476710.785490845393-0.2279635759780.74874761139432.622597673726.610861115730.7613297503
32.417101844920.941957625638-0.2900002509792.488804381060.05933401130211.25388924939-0.07882682472930.281631632316-0.10360374233-0.302711009120.087145903848-0.0424614592430.0652809338965-0.0436502156657-0.004555981205040.184033799681-0.01193521270010.009947179602430.154931262587-0.00778991335120.1338723499129.7337296507126.40969416255.83834341311
40.122513688545-0.0680673047008-0.131197977421.82903092611-1.007951908091.89921404279-0.1561924996020.1986558069220.464182711180.172282467701-0.105911265104-0.168831341585-0.210595339940.4626389735320.2680239300870.2453840271060.0131834273730.03884275801240.155212178394-0.06222447896280.13640431501524.200960984544.149695277425.1689067434
53.484777461650.1936617194371.386051276314.67356687189-0.4695314309048.67217605470.2724852242670.159356657637-0.2861401311050.752507610108-0.176294011657-0.1138641401930.944716564069-0.237665616648-0.1130314938850.6303671934930.0113969880988-0.09565548231930.407825136549-0.03667119418840.31257427565538.257894886935.17952375846.4524929193
62.33919375666-0.661947550858-1.980407795180.7258112170130.2757098291931.89579059812-0.0537071375323-0.1272916916970.142640380258-0.006486735784290.0473594690869-0.1336221539360.1404521350040.1827209362660.01428554993830.1903979027690.00252821138533-0.02025530249990.181905747875-0.000782935439350.17712703097715.899235446646.868201768828.1562291117
75.44081788781-0.9283380575982.677348397734.6515219956-1.216226444854.313975617260.370032927331-0.300187780562-0.387151114160.156324799939-0.128844809823-0.278163777960.433908395097-0.00556410618485-0.1707133112610.2889673004290.0010347202472-0.09493610053330.241702337030.0001992426480890.2173872538828.9937441869445.069539859953.0249141999
81.161904719320.696301220154-0.6022868056992.28010454713-0.8389993518681.215293153990.0986014597789-0.07436577278770.01168971521890.121280963681-0.0677596845908-0.00872737456518-0.04296077116990.000288519725545-0.03275539239950.160283915198-0.002944768472430.01621297345180.141811429869-0.01330235506230.1388935835764.6668905419444.027364026330.335605107
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'P' and (resid 1 through 10 )
2X-RAY DIFFRACTION2chain 'T' and (resid 7 through 16 )
3X-RAY DIFFRACTION3chain 'A' and (resid 300 through 467 )
4X-RAY DIFFRACTION4chain 'A' and (resid 468 through 521 )
5X-RAY DIFFRACTION5chain 'A' and (resid 522 through 586 )
6X-RAY DIFFRACTION6chain 'A' and (resid 587 through 676 )
7X-RAY DIFFRACTION7chain 'A' and (resid 677 through 743 )
8X-RAY DIFFRACTION8chain 'A' and (resid 744 through 876 )

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