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- PDB-6mu5: Bst DNA polymerase I TNA/DNA binary complex -

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Basic information

Entry
Database: PDB / ID: 6mu5
TitleBst DNA polymerase I TNA/DNA binary complex
Components
  • DNA (5'-D(P*GP*CP*GP*AP*TP*CP*AP*CP*GP*T)-3')
  • DNA polymerase I
  • TNA (5'-D(P*(TG)P*(TFT)P*(FA2)P*(TC)P*(TG)P*(TFT)P*(TG)P*(FA2)P*(TFT)P*(TC)P*(TG)P*(TC)P*(FA2))-3')
KeywordsTRANSFERASE/DNA / XNA reverse transcription / 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
Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / DNA polymerase 1 / Alpha-Beta Plaits - #370 / 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. ...Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / DNA polymerase 1 / Alpha-Beta Plaits - #370 / 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-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Alpha-Beta Plaits / DNA/RNA polymerase superfamily / Up-down Bundle / 2-Layer Sandwich / 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: 1.912 Å
AuthorsJackson, L.N. / Chim, N. / Chaput, J.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB: 1607111 United States
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Crystal structures of a natural DNA polymerase that functions as an XNA reverse transcriptase.
Authors: Jackson, L.N. / Chim, N. / Shi, C. / Chaput, J.C.
History
DepositionOct 22, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Aug 7, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 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*T)-3')
A: DNA polymerase I
T: TNA (5'-D(P*(TG)P*(TFT)P*(FA2)P*(TC)P*(TG)P*(TFT)P*(TG)P*(FA2)P*(TFT)P*(TC)P*(TG)P*(TC)P*(FA2))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,75410
Polymers73,0813
Non-polymers6727
Water5,368298
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.390, 93.280, 103.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: DNA chain DNA (5'-D(P*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: 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
#3: DNA chain TNA (5'-D(P*(TG)P*(TFT)P*(FA2)P*(TC)P*(TG)P*(TFT)P*(TG)P*(FA2)P*(TFT)P*(TC)P*(TG)P*(TC)P*(FA2))-3')


Mass: 3802.213 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / Source method: isolated from a natural source / Formula: H2O

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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: 3 Å3/Da / Density % sol: 59.01 %
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: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 9, 2017
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.91→66.84 Å / Num. obs: 65358 / % possible obs: 98.7 % / Redundancy: 19.7 % / CC1/2: 0.821 / Rmerge(I) obs: 0.718 / Net I/σ(I): 41.14
Reflection shellResolution: 1.91→1.98 Å / Rmerge(I) obs: 2.13 / CC1/2: 0.821

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1L3S

1l3s


Resolution: 1.912→66.839 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2251 2010 3.08 %
Rwork0.1907 --
obs0.1918 65328 98.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.912→66.839 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4644 460 35 298 5437
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075273
X-RAY DIFFRACTIONf_angle_d0.9767197
X-RAY DIFFRACTIONf_dihedral_angle_d7.8583048
X-RAY DIFFRACTIONf_chiral_restr0.054797
X-RAY DIFFRACTIONf_plane_restr0.005854
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.912-1.95980.39871370.34314086X-RAY DIFFRACTION91
1.9598-2.01280.34721340.27684423X-RAY DIFFRACTION98
2.0128-2.07210.27321440.23674475X-RAY DIFFRACTION98
2.0721-2.13890.28121350.20694512X-RAY DIFFRACTION99
2.1389-2.21540.24931450.19424493X-RAY DIFFRACTION99
2.2154-2.30410.2031430.18934502X-RAY DIFFRACTION99
2.3041-2.4090.25081420.19184503X-RAY DIFFRACTION99
2.409-2.5360.2551480.19164518X-RAY DIFFRACTION99
2.536-2.69490.21041440.19874519X-RAY DIFFRACTION99
2.6949-2.90290.2861440.20434607X-RAY DIFFRACTION100
2.9029-3.19510.24831440.20414559X-RAY DIFFRACTION100
3.1951-3.65740.20631490.17844628X-RAY DIFFRACTION100
3.6574-4.60770.18811440.15554646X-RAY DIFFRACTION100
4.6077-66.87950.18581570.18384847X-RAY DIFFRACTION100
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)
15.19210.34470.35033.37850.84593.63840.0579-0.642-0.6568-0.0331-0.16830.17340.6792-0.48540.11250.4349-0.0466-0.00210.43730.0690.3607-26.5668-16.238418.0893
22.4211-1.4105-0.08722.9521-0.36932.9664-0.1794-0.2275-0.12340.29190.13520.09370.13770.06970.03510.18470.03870.0080.1840.00620.2003-9.4998-20.476146.4872
31.6498-0.14041.53350.7916-0.13933.1344-0.0639-0.2429-0.0047-0.1435-0.01710.19920.0303-0.68520.0630.2997-0.02640.01820.2710.00270.2561-30.8222-7.128418.6839
40.8662-0.13050.20231.0066-0.32841.3916-0.03960.0990.0193-0.1387-0.05380.0535-0.2270.02980.09210.25970.0012-0.01760.2014-0.00430.2263-7.6864-1.807816.5011
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'P' and (resid 1 through 10 )
2X-RAY DIFFRACTION2chain 'A' and (resid 299 through 467 )
3X-RAY DIFFRACTION3chain 'A' and (resid 468 through 604 )
4X-RAY DIFFRACTION4chain 'A' and (resid 605 through 876 )

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