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- PDB-4yx5: SpaO(SPOA1,2) -

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Basic information

Entry
Database: PDB / ID: 4yx5
TitleSpaO(SPOA1,2)
Components(Surface presentation of antigens protein SpaO) x 2
KeywordsPROTEIN TRANSPORT / Type III Secretion System
Function / homology
Function and homology information


protein secretion by the type III secretion system / bacterial-type flagellum-dependent swarming motility / positive chemotaxis
Similarity search - Function
Surface presentation of antigens (SPOA) / SpoA-like / Type III secretion system apparatus protein YscQ/HrcQ/SpaO / Type III secretion system outer membrane, SpaO / Flagellar motor switch protein FliN-like, C-terminal domain / SpoA-like superfamily / Type III flagellar switch regulator (C-ring) FliN C-term / Roll / Mainly Beta
Similarity search - Domain/homology
Surface presentation of antigens protein SpaO
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9001 Å
AuthorsNotti, R.Q. / Stebbins, C.E.
CitationJournal: Nat Commun / Year: 2015
Title: A common assembly module in injectisome and flagellar type III secretion sorting platforms.
Authors: Notti, R.Q. / Bhattacharya, S. / Lilic, M. / Stebbins, C.E.
History
DepositionMar 22, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Feb 28, 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

Downloads & links

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Assembly

Deposited unit
A: Surface presentation of antigens protein SpaO
B: Surface presentation of antigens protein SpaO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9933
Polymers15,9572
Non-polymers351
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-28 kcal/mol
Surface area7950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.760, 65.760, 95.650
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-101-

CL

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Components

#1: Protein Surface presentation of antigens protein SpaO


Mass: 8246.572 Da / Num. of mol.: 1 / Fragment: UNP Residues 145-213
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: spaO, STM2891 / Production host: Escherichia coli (E. coli) / References: UniProt: P40699
#2: Protein Surface presentation of antigens protein SpaO


Mass: 7710.809 Da / Num. of mol.: 1 / Fragment: UNP Residues 232-297
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: spaO, STM2891 / Production host: Escherichia coli (E. coli) / References: UniProt: P40699
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl

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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: 3.44 Å3/Da / Density % sol: 64.26 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: SpaO(145-213) + SpaO (232-297) was concentrated to 12mg/mL and crystallized with 25% PEG400, 10% isopropanol, 100mM sodium citrate pH=5.6 at 277K. Microseeding was employed to enhance ...Details: SpaO(145-213) + SpaO (232-297) was concentrated to 12mg/mL and crystallized with 25% PEG400, 10% isopropanol, 100mM sodium citrate pH=5.6 at 277K. Microseeding was employed to enhance crystal uniformity and diffraction. Briefly, crystals to be seeded were harvested in precipitant solution and vortexed in a microfuge tube with a small stir bar for ~60 seconds. The slurry of microseeds was serially dilluted (5-10-fold steps) in precipitant solution and 5 selected microseed-precipitant mixtures were mixed with fresh protein as in a normal hanging drop experiment. Crystals were cryoprotected in mother liquor with the PEG400 concentration raised to 37.5%.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075, 0.979
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.0751
20.9791
ReflectionResolution: 2.9→54.19 Å / Num. obs: 4975 / % possible obs: 99.3 % / Redundancy: 24.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.034 / Net I/σ(I): 14.4 / Num. measured all: 122494 / Scaling rejects: 9
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.9-3.0826.21.4472.7202777750.8560.28399.3
8.7-54.1921.20.10926.945712160.9950.02495.2

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.2.7data scaling
PDB_EXTRACT3.15data extraction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.9001→38.678 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 28.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2791 497 10.01 %
Rwork0.2118 4467 -
obs0.2187 4964 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 154.08 Å2 / Biso mean: 74.2199 Å2 / Biso min: 37.22 Å2
Refinement stepCycle: final / Resolution: 2.9001→38.678 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms997 0 1 0 998
Biso mean--105.02 --
Num. residues----133
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011040
X-RAY DIFFRACTIONf_angle_d1.3241413
X-RAY DIFFRACTIONf_chiral_restr0.05168
X-RAY DIFFRACTIONf_plane_restr0.005181
X-RAY DIFFRACTIONf_dihedral_angle_d17.895377
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4 / % reflection obs: 99 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.9001-3.19190.36231190.254910781197
3.1919-3.65340.38261230.24610971220
3.6534-4.60180.24241220.189811071229
4.6018-38.68140.25871330.206911851318

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