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- PDB-6i89: Crystal structure of Antirestriction ArdC protein from R388 plasm... -

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Basic information

Entry
Database: PDB / ID: 6i89
TitleCrystal structure of Antirestriction ArdC protein from R388 plasmid. Metal-free structure.
ComponentsArdC protein
KeywordsMETAL BINDING PROTEIN / DNA binding protein Metalloprotease Antirestriction
Function / homologyN-terminal domain of anti-restriction factor ArdC / Antirestriction, ArdC / Polyvalent protein, metallopeptidase domain / N-terminal domain of anti-restriction factor ArdC / Zincin-like metallopeptidase / single-stranded DNA binding / metal ion binding / ArdC protein
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsGonzalez-Montes, L. / Moncalian, G.
Funding support Spain, 2items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBFU2014-55534-C2-2-P Spain
Spanish Ministry of Science, Innovation, and UniversitiesFPU014/0601 Spain
CitationJournal: Plos Genet. / Year: 2020
Title: ArdC, a ssDNA-binding protein with a metalloprotease domain, overpasses the recipient hsdRMS restriction system broadening conjugation host range.
Authors: Gonzalez-Montes, L. / Del Campo, I. / Garcillan-Barcia, M.P. / de la Cruz, F. / Moncalian, G.
History
DepositionNov 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1May 13, 2020Group: 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ArdC protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4823
Polymers33,2451
Non-polymers2362
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area500 Å2
ΔGint-17 kcal/mol
Surface area14450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.798, 136.798, 51.701
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3

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Components

#1: Protein ArdC protein


Mass: 33245.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: R388 plasmid / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ardC / Plasmid: pET29C / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6I6B2
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.8 Å3/Da / Density % sol: 56.08 % / Description: Triangular empty prism
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0,1 M HEPES pH 7,5; 10% w/v Polyethylene glycol 6,000 and 5% v/v (+/-)-2-Methyl-2,4-pentanediol. Cryoprotected with 20% 2-methyl-2 4-pentanediol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.99989 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99989 Å / Relative weight: 1
ReflectionResolution: 2→68.4 Å / Num. obs: 24347 / % possible obs: 99.81 % / Redundancy: 5.1 % / Biso Wilson estimate: 31.87 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.063 / Rrim(I) all: 0.07 / Net I/σ(I): 14.4
Reflection shellResolution: 2→2.072 Å / Rmerge(I) obs: 0.319 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 3505 / CC1/2: 0.889 / Rrim(I) all: 0.373 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
MOSFLM7.2.2data reduction
SCALA3.3.21data scaling
PHENIX1.11.1_2575phasing
RefinementMethod to determine structure: SAD / Resolution: 2→68.4 Å / SU ML: 0.2118 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 20.3625
RfactorNum. reflection% reflection
Rfree0.199 1230 5.05 %
Rwork0.1717 --
obs0.173 24340 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 36.4 Å2
Refinement stepCycle: LAST / Resolution: 2→68.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2189 0 16 207 2412
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00732258
X-RAY DIFFRACTIONf_angle_d0.84373056
X-RAY DIFFRACTIONf_chiral_restr0.0477316
X-RAY DIFFRACTIONf_plane_restr0.005396
X-RAY DIFFRACTIONf_dihedral_angle_d10.34931327
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.080.24331220.21382552X-RAY DIFFRACTION98.64
2.08-2.170.23541330.19152592X-RAY DIFFRACTION99.93
2.17-2.290.24411650.18692520X-RAY DIFFRACTION100
2.29-2.430.22561490.18862579X-RAY DIFFRACTION99.96
2.43-2.620.23421470.18752570X-RAY DIFFRACTION100
2.62-2.880.23751450.18412552X-RAY DIFFRACTION99.93
2.88-3.30.16791320.18042568X-RAY DIFFRACTION100
3.3-4.160.18951130.15262594X-RAY DIFFRACTION100
4.16-68.440.16271240.15842583X-RAY DIFFRACTION99.85

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