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- PDB-5u51: Structure of Francisella tularensis heterodimeric SspA (MglA-SspA... -

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Basic information

Entry
Database: PDB / ID: 5u51
TitleStructure of Francisella tularensis heterodimeric SspA (MglA-SspA) in complex with ppGpp
Components
  • Macrophage growth locus A
  • Stringent starvation protein A
KeywordsTRANSCRIPTION / Stringent starvation protein A / Macrophage growth locus A / ppGpp / GST-fold
Function / homology
Function and homology information


metal ion binding / cytoplasm
Similarity search - Function
: / Macrophage Locus Protein A, C-terminal domain / Stringent starvation protein A, C-terminal / : / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 ...: / Macrophage Locus Protein A, C-terminal domain / Stringent starvation protein A, C-terminal / : / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5',3'-TETRAPHOSPHATE / : / GST N-terminal domain-containing protein / Macrophage growth locus, subunit A / Stringent starvation protein A, regulator of transcription
Similarity search - Component
Biological speciesFrancisella tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsCuthbert, B.J. / Schumacher, M.A. / Brennan, R.G.
CitationJournal: Genes Dev. / Year: 2017
Title: Dissection of the molecular circuitry controlling virulence in Francisella tularensis.
Authors: Cuthbert, B.J. / Ross, W. / Rohlfing, A.E. / Dove, S.L. / Gourse, R.L. / Brennan, R.G. / Schumacher, M.A.
History
DepositionDec 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 1.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Stringent starvation protein A
A: Macrophage growth locus A
D: Stringent starvation protein A
B: Macrophage growth locus A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,60115
Polymers95,4094
Non-polymers2,19211
Water77543
1
C: Stringent starvation protein A
A: Macrophage growth locus A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,03110
Polymers47,7052
Non-polymers1,3268
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-26 kcal/mol
Surface area19030 Å2
MethodPISA
2
D: Stringent starvation protein A
B: Macrophage growth locus A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5705
Polymers47,7052
Non-polymers8663
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-21 kcal/mol
Surface area19390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.620, 111.560, 141.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 4 molecules CDAB

#1: Protein Stringent starvation protein A


Mass: 24110.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis (bacteria) / Gene: DR86_1150 / Plasmid: pMCSG21 / Details (production host): For coexpression / Cell line (production host): C41 (DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0E2ZL39, UniProt: Q5NHJ6*PLUS
#2: Protein Macrophage growth locus A


Mass: 23594.529 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis (bacteria) / Gene: DR86_1530 / Plasmid: pET28A
Details (production host): Expressed as an MBP fusion from pMCSG9
Cell line (production host): C41 (DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0E2ZLH6, UniProt: Q5NFG1*PLUS

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Non-polymers , 5 types, 54 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-G4P / GUANOSINE-5',3'-TETRAPHOSPHATE / guanosine tetraphosphate;ppGpp


Type: RNA linking / Mass: 603.160 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N5O17P4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.38 Å3/Da / Density % sol: 48.4 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: TRIS pH 8.5, PEG3350, ppGpp, magnesium chloride

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→87.61 Å / Num. obs: 23247 / % possible obs: 100 % / Redundancy: 5.4 % / Rsym value: 0.14 / Net I/σ(I): 7.8
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.874 / Mean I/σ(I) obs: 2 / Rpim(I) all: 0.404 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PUR, 1YY7

4pur

1yy7


Resolution: 2.8→87.61 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.28
RfactorNum. reflection% reflection
Rfree0.2648 1188 5.12 %
Rwork0.2124 --
obs0.2151 23184 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→87.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6184 0 136 43 6363
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036428
X-RAY DIFFRACTIONf_angle_d0.5268733
X-RAY DIFFRACTIONf_dihedral_angle_d13.0543914
X-RAY DIFFRACTIONf_chiral_restr0.0391031
X-RAY DIFFRACTIONf_plane_restr0.0041088
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8001-2.92760.37641460.29682710X-RAY DIFFRACTION100
2.9276-3.08190.34371430.28032695X-RAY DIFFRACTION100
3.0819-3.2750.37811490.27422711X-RAY DIFFRACTION100
3.275-3.52790.33041640.24892679X-RAY DIFFRACTION100
3.5279-3.88290.25321470.21112737X-RAY DIFFRACTION100
3.8829-4.44480.22881520.18352761X-RAY DIFFRACTION100
4.4448-5.59980.21011390.1812769X-RAY DIFFRACTION100
5.5998-87.65210.22541480.19142934X-RAY DIFFRACTION100

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