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- PDB-7k5u: Bst DNA polymerase I time-resolved structure, 48 hr post dATP and... -

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Basic information

Entry
Database: PDB / ID: 7k5u
TitleBst DNA polymerase I time-resolved structure, 48 hr post dATP and dCTP addition
Components
  • DNA (5'-D(P*CP*GP*AP*TP*CP*AP*CP*GP*TP*AP*C)-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
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*CP*GP*AP*TP*CP*AP*CP*GP*TP*AP*C)-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)75,0936
Polymers74,8053
Non-polymers2883
Water8,989499
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5260 Å2
ΔGint-59 kcal/mol
Surface area27950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.299, 93.491, 105.221
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*CP*GP*AP*TP*CP*AP*CP*GP*TP*AP*C)-3')


Mass: 3647.393 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)
#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.: 499 / 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: 57.14 %
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: 5.0.3 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→45.06 Å / Num. obs: 58064 / % possible obs: 98.2 % / Redundancy: 6.3 % / Biso Wilson estimate: 24.56 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.06405 / Rpim(I) all: 0.02798 / Rrim(I) all: 0.07008 / Net I/σ(I): 20.31
Reflection shellResolution: 2→2.071 Å / Rmerge(I) obs: 0.164 / Num. unique obs: 5685 / CC1/2: 0.959 / Rpim(I) all: 0.07411 / Rrim(I) all: 0.1805

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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→45.06 Å / SU ML: 0.2369 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.1784 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2295 1214 2.12 %
Rwork0.1898 55942 -
obs0.1907 57156 97.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.28 Å2
Refinement stepCycle: LAST / Resolution: 2→45.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4641 489 10 499 5639
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00745277
X-RAY DIFFRACTIONf_angle_d0.84237235
X-RAY DIFFRACTIONf_chiral_restr0.0517814
X-RAY DIFFRACTIONf_plane_restr0.005855
X-RAY DIFFRACTIONf_dihedral_angle_d10.6273146
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.080.2891250.24616168X-RAY DIFFRACTION97.61
2.08-2.170.25751400.19796238X-RAY DIFFRACTION98.64
2.17-2.290.28881120.28455278X-RAY DIFFRACTION83.55
2.29-2.430.22481340.18846258X-RAY DIFFRACTION98.76
2.43-2.620.25271440.19126296X-RAY DIFFRACTION98.97
2.62-2.880.2381400.19716290X-RAY DIFFRACTION99.01
2.88-3.30.23351360.19466358X-RAY DIFFRACTION99.07
3.3-4.160.23121350.17246402X-RAY DIFFRACTION99.03
4.16-45.060.18871480.16446654X-RAY DIFFRACTION99.34
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)
11.39803166363-0.269562449984-1.142831121740.7215567949890.6677864943932.02126994853-0.06248558909490.949785702232-0.365654075120.0609156447101-0.237307000705-0.04324334646580.558448566576-0.01329132689220.4265910585460.4722696917030.05289866159710.04009307306910.480838629015-0.1492626506780.4741141882427.609447410529.82883342532.8726458965
22.637772265220.0650788264990.3760906330910.809094975879-1.304828313062.22137538064-0.2949921630250.126714140152-0.3387150665320.7604652758920.361011095334-0.1460115179641.218113332180.3612880829-0.08359941754270.8135178136570.304983633951-0.0515926969140.397019647162-0.1033571313840.46123763594127.678354909228.105976943632.8468809651
31.531499928020.448596585576-0.2561750915691.44813306882-0.03124809193060.79730385534-0.03836092722560.15124289243-0.0581659811364-0.2109994777510.0582267484295-0.05468352490160.07904161839880.00264425535852-0.02320438290830.15331415443-0.005912362971680.008605370989440.144546241711-0.007162192648740.1268054006829.6956835805726.15348819195.69993573718
40.0823745802381-0.0366931441355-0.1402286400731.02849122305-0.4236708510381.14575634961-0.11121310289-0.02903228682270.2767005167020.0824255777542-0.0602923379807-0.114269684407-0.1121070090310.3422432689970.08170926371140.1810381299420.005363036663940.01807173894940.207279102885-0.0006452891835180.15605011174724.370147967843.674038305525.2437555905
50.178747846438-0.2469090575491.14918841810.7034260160830.1205651368522.356110726430.1223772397630.0121826024060.04135526438190.3272685833440.0434460387217-0.1048135679770.6115582060810.231707484015-0.06825173419510.4667854821550.043721905504-0.02036517515370.3629953813760.02864356935110.26137252804435.637341586337.002534332739.9506264391
60.577179662139-0.272064346713-0.4371525151690.7725247690160.1491923683861.037278926280.00868040254102-0.05911856924550.04167280292060.055259236061-0.0204453007652-0.128120776620.008282478992120.07806893347880.01733241836360.1489142890610.00232873118495-0.01899878757360.1388210912550.009637161790410.17112714650312.666179325547.115991566130.5973385971
72.556758457130.7277628914971.163394032251.20183825016-0.1328062369531.553668514370.176826110134-0.10918929323-0.3097540489590.176682029256-0.0614668505669-0.1339488343870.238952418338-0.0263956799356-0.08172045345660.2650549512290.0290671263984-0.05758291603380.227450299409-0.006055074741540.2558793828338.5986255778144.373881090653.0678365131
80.6922186767590.369999395306-0.3137181857561.32278922318-0.3751888421340.67927448020.0784281186459-0.03641998393580.02001992994030.144425727552-0.0622519346416-0.0179224154696-0.00918771929843-0.0088519163054-0.01351098549520.159035671375-0.005551645438970.00186620777390.148954046378-0.004304336141850.1327365365584.6735353770843.422602076130.1448940372
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'P' and (resid 2 through 12 )
2X-RAY DIFFRACTION2chain 'T' and (resid 3 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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