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- PDB-7k5r: Bst DNA polymerase I time-resolved structure, 120 min post dATP a... -

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Basic information

Entry
Database: PDB / ID: 7k5r
TitleBst DNA polymerase I time-resolved structure, 120 min post dATP addition
Components
  • DNA (5'-D(P*GP*CP*GP*AP*TP*CP*AP*CP*GP*TP*A)-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


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 / 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 ...DNA polymerase I, ribonuclease H-like domain / 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
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*GP*CP*GP*AP*TP*CP*AP*CP*GP*TP*A)-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)74,8046
Polymers74,5153
Non-polymers2883
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5350 Å2
ΔGint-61 kcal/mol
Surface area28050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.801, 93.188, 104.924
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(P*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(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)
#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.: 167 / 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: 2.88 Å3/Da / Density % sol: 57.3 %
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: 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: 2.3→45.72 Å / Num. obs: 38829 / % possible obs: 99.65 % / Redundancy: 6.6 % / Biso Wilson estimate: 37.12 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1415 / Rpim(I) all: 0.05906 / Rrim(I) all: 0.1537 / Net I/σ(I): 13.73
Reflection shellResolution: 2.3→2.382 Å / Rmerge(I) obs: 0.993 / Num. unique obs: 3812 / CC1/2: 0.786 / Rpim(I) all: 0.4601 / Rrim(I) all: 1.097

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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→45.72 Å / SU ML: 0.2863 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.9226 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2384 1998 5.15 %
Rwork0.1881 36796 -
obs0.1907 38794 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.53 Å2
Refinement stepCycle: LAST / Resolution: 2.3→45.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4636 494 15 167 5312
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00795289
X-RAY DIFFRACTIONf_angle_d0.90127253
X-RAY DIFFRACTIONf_chiral_restr0.0509815
X-RAY DIFFRACTIONf_plane_restr0.005857
X-RAY DIFFRACTIONf_dihedral_angle_d8.40684317
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.31241250.27382588X-RAY DIFFRACTION99.56
2.36-2.420.31151570.24922580X-RAY DIFFRACTION99.89
2.42-2.490.29141390.23572622X-RAY DIFFRACTION100
2.49-2.570.30921400.22732587X-RAY DIFFRACTION100
2.57-2.660.30491410.24662595X-RAY DIFFRACTION99.17
2.66-2.770.24031370.22422591X-RAY DIFFRACTION99.89
2.77-2.90.25131420.21612613X-RAY DIFFRACTION100
2.9-3.050.28631400.20382633X-RAY DIFFRACTION100
3.05-3.240.31171450.2042623X-RAY DIFFRACTION100
3.24-3.490.24381430.19472608X-RAY DIFFRACTION98.92
3.49-3.840.23281440.17732628X-RAY DIFFRACTION99.32
3.84-4.40.18481410.15212636X-RAY DIFFRACTION98.93
4.4-5.540.18431510.15162684X-RAY DIFFRACTION99.89
5.54-45.720.2061530.1662808X-RAY DIFFRACTION99.73
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)
18.1896295517-3.96803615197-4.152221825564.970212829325.127727740765.347567824450.2965566374551.4994147009-0.663894518832-0.131615871297-1.224376107310.1964529540591.51940101329-1.302275315750.8398409653730.9621184478470.0795876808380.05406266576940.870904209395-0.1417897504860.59123404917929.125723250228.111708405432.7644161927
26.245376369946.634614821784.468263297029.313583492250.9555453686759.54124571553-1.83205894316-1.30290312317-1.65086341942-1.05377983867-0.5728674695791.372417558161.16218843404-0.737991244152.149575336741.217952753490.3268850425470.4427665207470.787062886832-0.1093896758161.4323907564615.793646944143.359112561735.265851268
38.05010168249-0.5409797113782.0776462572.34041142368-0.6487742714521.094102644690.101194817206-0.0226299904542-1.683479840880.90727897560.0036755140390.4735585846631.981144477440.01378336385520.0230558015821.244462450170.227342986889-0.007851806939540.653238940595-0.1038882435580.68703925096329.347504558427.653050996231.6289595338
42.501298225380.671872879723-0.383716145133.208735107880.01619110112722.16958743967-0.086010828560.286307982403-0.128458419153-0.3533568625130.108689681168-0.01507939883210.1220699302810.0238760647763-0.007768509995390.284007278517-0.01244759178620.000947461703650.219146449971-0.007362182044040.2184416120929.7819045836226.26748240545.66296572336
50.0713280071067-0.124551597496-0.2195321789221.47006809124-1.091465114682.40954840681-0.1044713432020.3025317975950.4065774727830.213832823331-0.104485934897-0.154630699013-0.2686111729690.5736545113520.2247759632790.451459613850.02109365242380.03748268455870.187670944612-0.0699983748330.2405424065724.468353053843.731249039725.2338349323
61.29797543076-0.4435966928183.219926270411.75798728738-1.163989050938.611478873540.148268215744-0.0062684202236-0.04489727017590.5058657222270.0176517303286-0.1927072847680.5430333613710.257109325272-0.1281673209030.4976999816750.0520454290856-0.02219848883140.316568898999-0.001702916381540.39383684226535.733273990536.893018934639.838170014
73.07606593415-0.150220925927-2.186022629112.02921020187-0.1085787688582.348269628720.00570143689294-0.1943249743280.1295063353820.02240332128920.0155047496634-0.118909608950.03792053786760.193578027709-0.01050559053790.302736924423-0.002056723761-0.05197402569240.2166259426690.01286935433770.18426154419212.617901210647.231512045530.5551736304
87.73714304173-0.8294812837872.790757038125.91286823588-2.682564185864.731066976770.420736666075-0.311586583877-0.6216435273920.408345680287-0.123243784648-0.05115587152060.4390544943510.217628103125-0.2244669870480.4650426287140.0345324100261-0.1098016993350.286277281934-0.01915977739090.2957917241058.8264053951244.590252244352.71969122
91.519675150911.05248919849-0.9733951700043.07678327988-1.761148435192.131095370150.128256902709-0.06979410075280.02220746997470.0902944401576-0.0997525922955-0.0317809372766-0.07162350782670.00116687473939-0.01748744400090.281820029314-0.00643645250353-0.003138071762890.188269337028-0.02922941401890.1850998728194.6410934877943.662372625830.1404561664
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'P' and (resid 1 through 10 )
2X-RAY DIFFRACTION2chain 'P' and (resid 11 through 11 )
3X-RAY DIFFRACTION3chain 'T' and (resid 5 through 16 )
4X-RAY DIFFRACTION4chain 'A' and (resid 300 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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