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- PDB-6mu4: Bst DNA polymerase I FANA/DNA binary complex -

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Basic information

Entry
Database: PDB / ID: 6mu4
TitleBst DNA polymerase I FANA/DNA binary complex
Components
  • DNA (5'-D(P*GP*CP*GP*AP*TP*CP*AP*CP*GP*T)-3')
  • DNA polymerase I
  • FANA (5'-D(P*(UF2)P*(A5L)P*(CFL)P*(GFL)P*(UF2)P*(GFL)P*(A5L)P*(UF2)P*(CFL)P*(GFL)P*(CFL))-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: 1.62 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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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: FANA (5'-D(P*(UF2)P*(A5L)P*(CFL)P*(GFL)P*(UF2)P*(GFL)P*(A5L)P*(UF2)P*(CFL)P*(GFL)P*(CFL))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,0069
Polymers73,4353
Non-polymers5716
Water9,800544
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.835, 93.898, 105.809
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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DNA chain , 2 types, 2 molecules PT

#1: DNA chain DNA (5'-D(P*GP*CP*GP*AP*TP*CP*AP*CP*GP*T)-3')


Mass: 3349.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain FANA (5'-D(P*(UF2)P*(A5L)P*(CFL)P*(GFL)P*(UF2)P*(GFL)P*(A5L)P*(UF2)P*(CFL)P*(GFL)P*(CFL))-3')


Mass: 4183.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Protein , 1 types, 1 molecules A

#2: Protein DNA polymerase I / Bst DNA polymerase I


Mass: 65902.469 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 , 4 types, 550 molecules

#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 544 / 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: 3.05 Å3/Da / Density % sol: 59.68 %
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: 5.0.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 21, 2017
RadiationMonochromator: single crystal cylindrically bent Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.62→46.092 Å / Num. obs: 111377 / % possible obs: 99.73 % / Redundancy: 6.6 % / CC1/2: 1 / Rmerge(I) obs: 0.04112 / Net I/σ(I): 23.32
Reflection shellResolution: 1.62→1.67 Å / Rmerge(I) obs: 0.846 / Mean I/σ(I) obs: 2.22 / CC1/2: 0.824

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
autoXDSdata reduction
autoXDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1L3S

1l3s


Resolution: 1.62→46.092 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2105 2001 1.8 %
Rwork0.1874 --
obs0.1878 111224 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.62→46.092 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4632 503 35 544 5714
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065312
X-RAY DIFFRACTIONf_angle_d0.9367283
X-RAY DIFFRACTIONf_dihedral_angle_d20.8413072
X-RAY DIFFRACTIONf_chiral_restr0.056816
X-RAY DIFFRACTIONf_plane_restr0.005854
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.66050.24131480.25617689X-RAY DIFFRACTION100
1.6605-1.70540.26981310.24227707X-RAY DIFFRACTION100
1.7054-1.75560.24341590.23087683X-RAY DIFFRACTION100
1.7556-1.81230.25391230.22977770X-RAY DIFFRACTION100
1.8123-1.8770.23061470.21767747X-RAY DIFFRACTION100
1.877-1.95220.24361330.23977699X-RAY DIFFRACTION99
1.9522-2.04110.24341460.19827793X-RAY DIFFRACTION100
2.0411-2.14870.20391390.18647769X-RAY DIFFRACTION100
2.1487-2.28330.21431460.19287699X-RAY DIFFRACTION99
2.2833-2.45960.18961410.1857816X-RAY DIFFRACTION100
2.4596-2.7070.21841460.18667814X-RAY DIFFRACTION100
2.707-3.09870.22031440.19767895X-RAY DIFFRACTION100
3.0987-3.90370.20531460.16917936X-RAY DIFFRACTION100
3.9037-46.11070.18831520.1698206X-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)
15.573-0.30972.68456.91280.00144.25190.38090.7322-0.6489-0.62350.0941-0.35010.8268-0.7211-0.44470.9725-0.1702-0.07460.95820.07290.600530.351427.545432.9512
20.0208-0.02260.02350.0553-0.02760.03510.00630.0132-0.0091-0.005-0.0396-0.02940.0270.02120.00011.23660.1050.02970.99790.00331.082215.410438.855736.0897
32.0810.87-0.31932.54020.07521.2079-0.07740.1932-0.105-0.29630.0745-0.1470.0634-0.00410.00250.1946-0.00080.01630.1842-0.0150.17939.677126.28745.9624
40.1216-0.02590.22851.2826-0.551.5168-0.11070.15290.29710.1435-0.0959-0.1557-0.13870.36640.21610.18060.01840.02110.175-0.01570.172323.991644.114625.3809
51.9104-0.80394.54281.1768-1.92257.31180.1534-0.0554-0.02190.3756-0.0835-0.10230.1199-0.0338-0.07880.45420.0178-0.02150.45310.06480.377236.757937.267140.125
64.1533.3886-1.3266.7105-0.75650.89180.36-0.44980.08090.5057-0.3381-0.2296-0.05110.2651-0.04730.19170.00150.01440.26750.02330.212519.918545.233826.096
70.81640.24720.15691.4377-0.39061.64050.0443-0.2574-0.06230.2703-0.0658-0.27840.16090.07810.02660.21930.0025-0.05360.20210.00010.2186.858146.653947.9444
81.09780.3489-0.7031.8531-0.87311.34470.0681-0.07060.0050.0594-0.0832-0.0145-0.03240.06150.01590.1522-0.01410.00160.1719-0.01270.16424.719343.859630.3445
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 '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 646 )
7X-RAY DIFFRACTION7chain 'A' and (resid 647 through 743 )
8X-RAY DIFFRACTION8chain 'A' and (resid 744 through 876 )

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