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- PDB-4yxa: Complex of SpaO(SPOA1,2 SeMet) and OrgB(APAR)::T4lysozyme fusion ... -

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Basic information

Entry
Database: PDB / ID: 4yxa
TitleComplex of SpaO(SPOA1,2 SeMet) and OrgB(APAR)::T4lysozyme fusion protein
Components
  • (Surface presentation of antigens protein SpaO) x 2
  • Oxygen-regulated invasion protein OrgB,Endolysin
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 / viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / protein transport / host cell cytoplasm ...protein secretion by the type III secretion system / bacterial-type flagellum-dependent swarming motility / positive chemotaxis / viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / protein transport / host cell cytoplasm / defense response to bacterium / cytoplasm
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 / Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme ...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 / Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Lysozyme / Lysozyme-like domain superfamily / Roll / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Endolysin / SPI-1 type 3 secretion system stator protein / Surface presentation of antigens protein SpaO
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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 1.2Sep 27, 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
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
C: Oxygen-regulated invasion protein OrgB,Endolysin
D: Surface presentation of antigens protein SpaO
E: Surface presentation of antigens protein SpaO
F: Oxygen-regulated invasion protein OrgB,Endolysin


Theoretical massNumber of molelcules
Total (without water)76,5216
Polymers76,5216
Non-polymers00
Water2,198122
1
A: Surface presentation of antigens protein SpaO
B: Surface presentation of antigens protein SpaO
C: Oxygen-regulated invasion protein OrgB,Endolysin


Theoretical massNumber of molelcules
Total (without water)38,2613
Polymers38,2613
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5890 Å2
ΔGint-38 kcal/mol
Surface area16530 Å2
MethodPISA
2
D: Surface presentation of antigens protein SpaO
E: Surface presentation of antigens protein SpaO
F: Oxygen-regulated invasion protein OrgB,Endolysin


Theoretical massNumber of molelcules
Total (without water)38,2613
Polymers38,2613
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5670 Å2
ΔGint-35 kcal/mol
Surface area16410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.880, 88.500, 63.320
Angle α, β, γ (deg.)90.000, 116.070, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Surface presentation of antigens protein SpaO


Mass: 8246.572 Da / Num. of mol.: 2 / 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: 7851.493 Da / Num. of mol.: 2 / 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: Protein Oxygen-regulated invasion protein OrgB,Endolysin / Lysis protein / Lysozyme / Muramidase


Mass: 22162.568 Da / Num. of mol.: 2 / Fragment: UNP Residues 1-30,UNP Residues 1-30 / Mutation: D20N, C54T, C97A,D20N, C54T, C97A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria), (gene. exp.) Enterobacteria phage T4 (virus)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: orgB, STM2869 / Production host: Escherichia coli (E. coli) / References: UniProt: P0CL45, UniProt: P00720, lysozyme
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.15 Å3/Da / Density % sol: 42.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: SpaO(145-213, SeMet) + SpaO (232-297, SeMet) + OrgB(1-30)::T4 lysozyme (native) was concentrated to 18mg/mL, supplemented with 50mM maltose, and crystallized with 25% PEG3350, 200mM ammonium ...Details: SpaO(145-213, SeMet) + SpaO (232-297, SeMet) + OrgB(1-30)::T4 lysozyme (native) was concentrated to 18mg/mL, supplemented with 50mM maltose, and crystallized with 25% PEG3350, 200mM ammonium formate, 100mM sodium acetate pH=5.0. 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 25% PEG3350, 10% ethylene glycol, 200mM ammonium formate, 100mM sodium acetate pH=5.0, 50mM maltose.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
Reflection twinOperator: l,-k,h / Fraction: 0.28
ReflectionResolution: 2.35→47.61 Å / Num. obs: 25759 / % possible obs: 99 % / Redundancy: 6.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.037 / Net I/σ(I): 12.8 / Num. measured all: 169948 / Scaling rejects: 92
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
2.35-2.436.60.6172.61680925350.8160.25699.6
9.1-47.616.40.05629.525934060.9970.02386.5

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.2.7data scaling
PDB_EXTRACT3.15data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YX7

4yx7


Resolution: 2.35→45.804 Å / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 35.43 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2618 1619 6.29 %
Rwork0.1984 24137 -
obs0.2027 25740 98.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 132.27 Å2 / Biso mean: 46.8298 Å2 / Biso min: 19.12 Å2
Refinement stepCycle: final / Resolution: 2.35→45.804 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4810 0 0 122 4932
Biso mean---45.62 -
Num. residues----618
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114893
X-RAY DIFFRACTIONf_angle_d1.4646624
X-RAY DIFFRACTIONf_chiral_restr0.054774
X-RAY DIFFRACTIONf_plane_restr0.007843
X-RAY DIFFRACTIONf_dihedral_angle_d17.4291804
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3501-2.4260.35851320.28842200233294
2.426-2.51260.30751720.28342186235892
2.5126-2.61320.38321330.29022198233194
2.6132-2.73210.3491400.2822205234593
2.7321-2.8760.32061440.26322198234293
2.876-3.05610.30841500.24732185233593
3.0561-3.29190.24591580.23122201235993
3.2919-3.62280.27081460.2052171231793
3.6228-4.14620.21271450.16572206235192
4.1462-5.22060.19291410.13572190233192
5.2206-33.40810.27881390.1652197233691

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