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- PDB-5u56: Structure of Francisella tularensis heterodimeric SspA (MglA-SspA) -

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Basic information

Entry
Database: PDB / ID: 5u56
TitleStructure of Francisella tularensis heterodimeric SspA (MglA-SspA)
Components
  • Macrophage growth locus A
  • Stringent starvation protein A
KeywordsTRANSCRIPTION / Stringent starvation protein A / Macrophage growth locus A / 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 Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal ...: / 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 Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / 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
PROLINE / : / 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: 2.65 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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)96,94517
Polymers95,4094
Non-polymers1,53613
Water1,13563
1
C: Stringent starvation protein A
A: Macrophage growth locus A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6659
Polymers47,7052
Non-polymers9607
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-14 kcal/mol
Surface area19300 Å2
MethodPISA
2
D: Stringent starvation protein A
B: Macrophage growth locus A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2808
Polymers47,7052
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-8 kcal/mol
Surface area19810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.408, 113.261, 140.400
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 protein 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 , 4 types, 76 molecules

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


Mass: 92.094 Da / Num. of mol.: 9 / 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-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.77 Å3/Da / Density % sol: 55.55 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEGRX2 17 L-proline, HEPES, PEG 1500

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 31478 / % possible obs: 99.9 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 31.74
Reflection shellResolution: 2.65→2.7 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.784 / Mean I/σ(I) obs: 2.13 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PUR, 1YY7

4pur

1yy7


Resolution: 2.65→44.077 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2587 1589 5.06 %
Rwork0.2045 --
obs0.2073 31406 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.65→44.077 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6220 0 93 63 6376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026413
X-RAY DIFFRACTIONf_angle_d0.5658671
X-RAY DIFFRACTIONf_dihedral_angle_d18.5582408
X-RAY DIFFRACTIONf_chiral_restr0.041022
X-RAY DIFFRACTIONf_plane_restr0.0041089
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.73560.39261350.29112606X-RAY DIFFRACTION98
2.7356-2.83330.34281370.27222681X-RAY DIFFRACTION100
2.8333-2.94670.35441340.27252664X-RAY DIFFRACTION100
2.9467-3.08080.33021370.26242694X-RAY DIFFRACTION100
3.0808-3.24320.33741450.25252697X-RAY DIFFRACTION100
3.2432-3.44630.29141430.23442696X-RAY DIFFRACTION100
3.4463-3.71230.2671470.22452704X-RAY DIFFRACTION100
3.7123-4.08560.25891500.19272713X-RAY DIFFRACTION100
4.0856-4.67620.2571480.17112729X-RAY DIFFRACTION100
4.6762-5.88940.20651450.18632764X-RAY DIFFRACTION100
5.8894-44.08260.20611680.1722869X-RAY DIFFRACTION99

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