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- PDB-6us5: DNA polymerase I Large Fragment from Bacillus stearothermophilus ... -

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Basic information

Entry
Database: PDB / ID: 6us5
TitleDNA polymerase I Large Fragment from Bacillus stearothermophilus with DNA template, 3'-amino primer, dGpNHpp analog, and Mn2+
Components
  • DNA (5'-D(*CP*AP*CP*GP*CP*TP*GP*AP*TP*CP*GP*CP*A)-3')
  • DNA (5'-D(*GP*CP*GP*AP*TP*CP*AP*GP*(C42))-3')
  • DNA polymerase I
KeywordsREPLICATION/DNA / DNA polymerase / 3'-amino terminal primer / GpNHpp / Mn2+ / REPLICATION-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 / Alpha-Beta Plaits - #370 / 3'-5' exonuclease / 3'-5' exonuclease domain / DNA polymerase A / DNA polymerase family A ...: / DNA polymerase I, ribonuclease H-like domain / DNA polymerase 1 / Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / 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
: / Chem-XG4 / DNA / DNA (> 10) / DNA polymerase I
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsZhang, W. / Lelyveld, V.S. / Szostak, J.W.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Synthesis of phosphoramidate-linked DNA by a modified DNA polymerase.
Authors: Lelyveld, V.S. / Zhang, W. / Szostak, J.W.
History
DepositionOct 24, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1May 27, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 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
A: DNA polymerase I
B: DNA (5'-D(*GP*CP*GP*AP*TP*CP*AP*GP*(C42))-3')
C: DNA (5'-D(*CP*AP*CP*GP*CP*TP*GP*AP*TP*CP*GP*CP*A)-3')
D: DNA polymerase I
E: DNA (5'-D(*GP*CP*GP*AP*TP*CP*AP*GP*(C42))-3')
F: DNA (5'-D(*CP*AP*CP*GP*CP*TP*GP*AP*TP*CP*GP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,29517
Polymers145,5006
Non-polymers1,79511
Water7,386410
1
A: DNA polymerase I
B: DNA (5'-D(*GP*CP*GP*AP*TP*CP*AP*GP*(C42))-3')
C: DNA (5'-D(*CP*AP*CP*GP*CP*TP*GP*AP*TP*CP*GP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,79210
Polymers72,7503
Non-polymers1,0417
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6320 Å2
ΔGint-73 kcal/mol
Surface area27530 Å2
MethodPISA
2
D: DNA polymerase I
E: DNA (5'-D(*GP*CP*GP*AP*TP*CP*AP*GP*(C42))-3')
F: DNA (5'-D(*CP*AP*CP*GP*CP*TP*GP*AP*TP*CP*GP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5037
Polymers72,7503
Non-polymers7534
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-47 kcal/mol
Surface area27560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.761, 108.805, 149.969
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AD

#1: Protein DNA polymerase I


Mass: 66073.750 Da / Num. of mol.: 2 / Mutation: D598A/F710Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Strain: Strain X / Gene: DPO1, polA / Production host: Escherichia coli (E. coli) / References: UniProt: D9N168, DNA-directed DNA polymerase

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DNA chain , 2 types, 4 molecules BECF

#2: DNA chain DNA (5'-D(*GP*CP*GP*AP*TP*CP*AP*GP*(C42))-3')


Mass: 2739.827 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*CP*AP*CP*GP*CP*TP*GP*AP*TP*CP*GP*CP*A)-3')


Mass: 3936.575 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 421 molecules

#4: Chemical ChemComp-XG4 / 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine


Mass: 506.196 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C10H17N6O12P3
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#6: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 410 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.63 Å3/Da / Density % sol: 53.19 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.4
Details: 0.1 M MES, pH 5.4, 2M ammonium sulfate, 10 mM MnSO4, 5 % MPD

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Data collection

DiffractionMean temperature: 99 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Sep 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 72498 / % possible obs: 98.4 % / Redundancy: 3.6 % / CC1/2: 0.966 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.076 / Rrim(I) all: 0.147 / Χ2: 0.828 / Net I/σ(I): 10
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.605 / Mean I/σ(I) obs: 2.67 / Num. unique obs: 6573 / CC1/2: 0.752 / Rpim(I) all: 0.379 / Rrim(I) all: 0.717 / Χ2: 1.125 / % possible all: 90.4

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1L5U

1l5u


Resolution: 2.25→47.06 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2784 3607 4.98 %
Rwork0.2242 68829 -
obs0.2269 72436 98.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 155.03 Å2 / Biso mean: 50.8868 Å2 / Biso min: 14.68 Å2
Refinement stepCycle: final / Resolution: 2.25→47.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9292 839 99 410 10640
Biso mean--67.7 38.56 -
Num. residues----1202
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.25-2.280.6746800.66841898197870
2.28-2.310.3481410.34812622276399
2.31-2.340.33581200.294726712791100
2.34-2.370.34631350.275926712806100
2.37-2.410.31461370.266426622799100
2.41-2.450.33041670.26612610277799
2.45-2.490.3231470.250426662813100
2.49-2.540.27991550.247726502805100
2.54-2.590.32391510.251226522803100
2.59-2.640.33141330.24526772810100
2.64-2.70.31531340.250826722806100
2.7-2.760.29381580.253826722830100
2.76-2.830.34051500.253126602810100
2.83-2.910.32261300.240926632793100
2.91-2.990.3091180.236727312849100
2.99-3.090.28151480.226126612809100
3.09-3.20.3181370.229327122849100
3.2-3.330.30851400.220526852825100
3.33-3.480.28251410.215526992840100
3.48-3.660.29611330.22832604273797
3.66-3.890.32031470.23962628277597
3.89-4.190.20841290.18962588271795
4.19-4.610.22171330.168727292862100
4.61-5.280.24331460.177327452891100
5.28-6.650.23481380.19672770290899
6.65-47.060.20371590.17842831299098

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