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- PDB-8dgl: Crystal Structure of the RdfS Excisionase -

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Basic information

Entry
Database: PDB / ID: 8dgl
TitleCrystal Structure of the RdfS Excisionase
ComponentsRecombination Directionality Factor RdfS
KeywordsDNA BINDING PROTEIN / Excisionase / Recombination Directionality Factor / winged helix-turn-helix / superhelix
Function / homologyHelix-turn-helix domain, group 17 / Helix-turn-helix domain / Putative DNA-binding domain superfamily / DNA binding / DNA-binding protein
Function and homology information
Biological speciesMesorhizobium japonicum R7A (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.45 Å
AuthorsVerdonk, C.J. / Ramsay, J.P. / Marshall, A.C. / Bond, C.S.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)FT170100235 Australia
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Crystallographic and X-ray scattering study of RdfS, a recombination directionality factor from an integrative and conjugative element.
Authors: Verdonk, C.J. / Marshall, A.C. / Ramsay, J.P. / Bond, C.S.
History
DepositionJun 24, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Apr 3, 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: Recombination Directionality Factor RdfS
B: Recombination Directionality Factor RdfS
C: Recombination Directionality Factor RdfS
D: Recombination Directionality Factor RdfS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,26211
Polymers39,8444
Non-polymers4187
Water3,189177
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Multiple peaks beyond monomer molecular weight
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.251, 119.204, 123.397
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Recombination Directionality Factor RdfS


Mass: 9960.901 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesorhizobium japonicum R7A (bacteria) / Gene: msi109, A8146_15230, BAE39_30655, EB815_31145 / Plasmid: pETM11 / Production host: Escherichia coli (E. coli) / Strain (production host): NiCo21(DE3) / References: UniProt: Q7AL96
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.25 Å3/Da / Density meas: 518521.6 Mg/m3 / Density % sol: 62.19 % / Description: Multi-nuclear small needle-like
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.05 M MES; pH 6.5, 4% w/v PEG 5000 MME, 5% v/v 1-propanol, 0.1 M sodium citrate; RdfS protein at 4.3 mg/mL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953 Å / Relative weight: 1
ReflectionResolution: 2.45→42.87 Å / Num. obs: 19949 / % possible obs: 99.4 % / Redundancy: 6.6 % / Biso Wilson estimate: 41.59 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.06 / Rrim(I) all: 0.155 / Net I/σ(I): 9 / Num. measured all: 132047 / Scaling rejects: 21
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.45-2.556.70.8551410821180.7440.3540.9272.494.7
8.83-42.875.60.10728185010.9880.0470.11716.499.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.31 Å42.87 Å
Translation5.31 Å42.87 Å

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Processing

Software
NameVersionClassification
PHENIX1.19.2refinement
XDSNov 1, 2016data reduction
Aimless0.7.7data scaling
PHASER2.8.3phasing
MOLREP11.7.03phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: alphafold prediction

Resolution: 2.45→42.87 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2456 933 4.69 %Random selection
Rwork0.1993 18958 --
obs0.2015 19891 99.39 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.6 Å2 / Biso mean: 44.7947 Å2 / Biso min: 23.63 Å2
Refinement stepCycle: final / Resolution: 2.45→42.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2160 0 22 177 2359
Biso mean--60.44 46.16 -
Num. residues----270
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.45-2.580.32131210.26462574269596
2.58-2.740.29831290.237426742803100
2.74-2.950.29651610.254126602821100
2.95-3.250.31831180.220626952813100
3.25-3.720.251400.200826902830100
3.72-4.680.20921240.157627502874100
4.68-42.870.19751400.186629153055100

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