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- PDB-8a1b: TraI trans-esterase domain from pKM101 (apo) -

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Basic information

Entry
Database: PDB / ID: 8a1b
TitleTraI trans-esterase domain from pKM101 (apo)
ComponentsTraI
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 / AAA domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1196
Polymers34,7531
Non-polymers3675
Water3,567198
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.166, 80.628, 90.575
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: 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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 41.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 10% PEG 4000, 20% glycerol, 0.03M MgCl2, 0.03M CaCl, 0.1M MOPS/HEPES-Na pH 7.5

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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 PILATUS3 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: 1.7→60.22 Å / Num. obs: 33141 / % possible obs: 99.91 % / Redundancy: 2 % / Biso Wilson estimate: 23.56 Å2 / CC1/2: 0.999 / Net I/σ(I): 12.42
Reflection shellResolution: 1.7→1.761 Å / Num. unique obs: 3253 / CC1/2: 0.782

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
AutoProcessGrenADESdata processing
PHENIX1.20.1_4487phasing
Coot0.9.6model building
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3L6T

3l6t


Resolution: 1.7→60.22 Å / SU ML: 0.2279 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.4816
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1946 1706 5.15 %
Rwork0.1735 31432 -
obs0.1746 33138 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.54 Å2
Refinement stepCycle: LAST / Resolution: 1.7→60.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2351 0 20 198 2569
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012432
X-RAY DIFFRACTIONf_angle_d1.01573270
X-RAY DIFFRACTIONf_chiral_restr0.0575353
X-RAY DIFFRACTIONf_plane_restr0.0105428
X-RAY DIFFRACTIONf_dihedral_angle_d5.9067335
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.750.36911470.32112600X-RAY DIFFRACTION99.78
1.75-1.810.31891460.27492545X-RAY DIFFRACTION99.89
1.81-1.870.26621570.22252550X-RAY DIFFRACTION99.85
1.87-1.950.21441410.18272572X-RAY DIFFRACTION99.93
1.95-2.030.21511390.17052598X-RAY DIFFRACTION99.96
2.03-2.140.17561390.1732595X-RAY DIFFRACTION99.93
2.14-2.280.22071430.17412604X-RAY DIFFRACTION99.89
2.28-2.450.19371400.15592597X-RAY DIFFRACTION99.96
2.45-2.70.17721420.15422634X-RAY DIFFRACTION99.96
2.7-3.090.19021320.15942649X-RAY DIFFRACTION99.93
3.09-3.890.16651500.14932659X-RAY DIFFRACTION100
3.89-60.220.17481300.17932829X-RAY DIFFRACTION99.83
Refinement TLS params.Method: refined / Origin x: 0.987883145146 Å / Origin y: 12.0831726436 Å / Origin z: 20.6681037459 Å
111213212223313233
T0.107812488718 Å20.013213469618 Å20.006132311458 Å2-0.115286313232 Å2-0.00714582305524 Å2--0.120025103422 Å2
L0.69345131456 °20.256037001237 °20.199513313862 °2-0.752964489014 °2-0.0560252044737 °2--0.805646267495 °2
S-0.0173540526104 Å °0.0584287356401 Å °0.0364964693479 Å °-0.0345037851458 Å °0.0325420197695 Å °0.0672152800589 Å °-0.0423599033591 Å °-0.00309771919612 Å °-0.0150776210009 Å °
Refinement TLS groupSelection details: all

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