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- PDB-6pdk: The Structure of Smlt3025, an immunity protein of the Stenotropho... -

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Basic information

Entry
Database: PDB / ID: 6pdk
TitleThe Structure of Smlt3025, an immunity protein of the Stenotrophomonas maltophilia type IV secretion system
ComponentsUncharacterized protein
KeywordsANTITOXIN / Type IV Secretion System / Bacterial competition
Function / homologyBROMIDE ION / Uncharacterized protein
Function and homology information
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsMatsuyama, B.Y. / Farah, C.S.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a Tecnologia2017/17303-7 Brazil
Fundacao para a Ciencia e a Tecnologia2016/00458-5 Brazil
CitationJournal: Plos Pathog. / Year: 2019
Title: The opportunistic pathogen Stenotrophomonas maltophilia utilizes a type IV secretion system for interbacterial killing.
Authors: Bayer-Santos, E. / Cenens, W. / Matsuyama, B.Y. / Oka, G.U. / Di Sessa, G. / Mininel, I.D.V. / Alves, T.L. / Farah, C.S.
History
DepositionJun 19, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2019Group: Data collection / 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 / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,50716
Polymers30,4861
Non-polymers1,02115
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.532, 67.532, 149.386
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3
Components on special symmetry positions
IDModelComponents
11A-414-

BR

21A-617-

HOH

31A-626-

HOH

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Components

#1: Protein Uncharacterized protein


Mass: 30486.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stenotrophomonas maltophilia (strain K279a) (bacteria)
Strain: K279a / Gene: Smlt3025 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B2FJJ6
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Br
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.33 Å3/Da / Density % sol: 47.12 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Imidazole/MES Monohydrate pH 6.5 0.03M Sodium Fluoride 0.03M Sodium Bromide 0.03M Sodium Iodide 12.5% MPD 12.5% PEG10000 12.5% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.5419 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 1.9→46.05 Å / Num. obs: 19897 / % possible obs: 99.4 % / Redundancy: 4.8 % / Biso Wilson estimate: 33.03 Å2 / Net I/σ(I): 14.3
Reflection shellResolution: 1.9→1.91 Å / Num. unique obs: 3140

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→21.87 Å / SU ML: 0.281 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 27.7952
RfactorNum. reflection% reflection
Rfree0.2486 1988 10 %
Rwork0.1951 --
obs0.2003 19881 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 39.65 Å2
Refinement stepCycle: LAST / Resolution: 1.9→21.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1984 0 15 149 2148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00752046
X-RAY DIFFRACTIONf_angle_d0.93612778
X-RAY DIFFRACTIONf_chiral_restr0.058295
X-RAY DIFFRACTIONf_plane_restr0.006371
X-RAY DIFFRACTIONf_dihedral_angle_d24.332797
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.38711350.30321183X-RAY DIFFRACTION91.78
1.95-20.30111470.24271260X-RAY DIFFRACTION99.72
2-2.060.2881420.23071310X-RAY DIFFRACTION99.79
2.06-2.130.30391430.23171288X-RAY DIFFRACTION100
2.13-2.20.33621370.23221290X-RAY DIFFRACTION99.86
2.2-2.290.2681390.22521283X-RAY DIFFRACTION100
2.29-2.390.3111420.22511289X-RAY DIFFRACTION100
2.39-2.520.29961410.21921284X-RAY DIFFRACTION100
2.52-2.680.28221390.21231277X-RAY DIFFRACTION99.93
2.68-2.880.27041470.22021292X-RAY DIFFRACTION100
2.88-3.170.25671410.20871296X-RAY DIFFRACTION100
3.17-3.630.21991410.17741262X-RAY DIFFRACTION100
3.63-4.570.22841440.16171298X-RAY DIFFRACTION100
4.57-21.870.19291500.17181281X-RAY DIFFRACTION99.79

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