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- PDB-8a1c: TraI trans-esterase domain from pKM101 (DNA bound) -

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Basic information

Entry
Database: PDB / ID: 8a1c
TitleTraI trans-esterase domain from pKM101 (DNA bound)
Components
  • 11mer oriT DNA
  • TraI
KeywordsDNA BINDING PROTEIN / Relaxase / Trans-esterase
Function / homology
Function and homology information


Conjugative relaxase, N-terminal / TrwC relaxase / TrwC relaxase / UvrD-like helicase C-terminal domain / UvrD-like helicase C-terminal domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
: / DNA / DNA (> 10) / TraI
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBreidenstein, A. / Berntsson, R.P.-A.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation Sweden
Swedish Research Council2016-03599 Sweden
CitationJournal: Life Sci Alliance / Year: 2023
Title: Structural and functional characterization of TraI from pKM101 reveals basis for DNA processing.
Authors: Breidenstein, A. / Ter Beek, J. / Berntsson, R.P.
History
DepositionJun 1, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TraI
C: 11mer oriT DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2283
Polymers38,1732
Non-polymers551
Water64936
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.444, 81.643, 90.785
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
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: Protein TraI /


Mass: 34752.801 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: traI / Production host: Escherichia coli (E. coli) / References: UniProt: D9Z5Q2
#2: DNA chain 11mer oriT DNA


Mass: 3420.231 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O
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: 2.11 Å3/Da / Density % sol: 41.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 10% PEG 20000, 20% PEG MME 550, 0.3 M sodium nitrate, 0.03 M disodium hydrogen phosphate, 0.03 M ammonium sulfate, 0.1 M MES/imidazole pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.974 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.974 Å / Relative weight: 1
ReflectionResolution: 2.1→40.82 Å / Num. obs: 19496 / % possible obs: 99.85 % / Redundancy: 2 % / Biso Wilson estimate: 41.44 Å2 / CC1/2: 0.996 / Net I/σ(I): 9.16
Reflection shellResolution: 2.1→2.175 Å / Redundancy: 2 % / Num. unique obs: 1908 / CC1/2: 0.751 / % possible all: 99.79

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
Coot0.9.6model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3L6T

3l6t


Resolution: 2.1→40.82 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2672 995 5.11 %
Rwork0.2252 18483 -
obs0.2273 19478 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 214.49 Å2 / Biso mean: 67.1356 Å2 / Biso min: 30.48 Å2
Refinement stepCycle: final / Resolution: 2.1→40.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2403 208 1 36 2648
Biso mean--39.89 51.46 -
Num. residues----311
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.1-2.210.33741210.328125992720
2.21-2.350.32741390.293125812720
2.35-2.530.33311350.282226092744
2.53-2.790.341490.263526182767
2.79-3.190.31731600.25226072767
3.19-4.020.23521550.207826582813
4.02-40.820.21951360.188428112947
Refinement TLS params.Method: refined / Origin x: 3.3439 Å / Origin y: 10.8771 Å / Origin z: 22.3112 Å
111213212223313233
T0.4127 Å20.0168 Å20.0353 Å2-0.2701 Å20.0054 Å2--0.2805 Å2
L1.7344 °20.2392 °20.9923 °2-1.0051 °20.4181 °2--3.1306 °2
S-0.0621 Å °0.0129 Å °0.0396 Å °-0.0221 Å °0.0018 Å °0.0168 Å °-0.0486 Å °0.08 Å °0.0746 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 305
2X-RAY DIFFRACTION1allC2 - 11
3X-RAY DIFFRACTION1allB1
4X-RAY DIFFRACTION1allS1 - 41

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