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- PDB-4yx7: Complex of SpaO(SPOA1,2) and OrgB(APAR)::T4lysozyme fusion protein -

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Basic information

Entry
Database: PDB / ID: 4yx7
TitleComplex of SpaO(SPOA1,2) 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: 2.0007 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

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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)76,2406
Polymers76,2406
Non-polymers00
Water11,836657
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)38,1203
Polymers38,1203
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6080 Å2
ΔGint-39 kcal/mol
Surface area16570 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)38,1203
Polymers38,1203
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5890 Å2
ΔGint-36 kcal/mol
Surface area16450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.092, 89.070, 62.092
Angle α, β, γ (deg.)90.000, 114.940, 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: 7710.809 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.: 657 / 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: 2.1 Å3/Da / Density % sol: 41.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: SpaO(145-213) + SpaO (232-297) + OrgB(1-30)::T4 lysozyme was concentrated to 18.5mg/mL and crystallized with 25% PEG3350, 200mM ammonium formate, 100mM sodium acetate pH=5.0. Microseeding ...Details: SpaO(145-213) + SpaO (232-297) + OrgB(1-30)::T4 lysozyme was concentrated to 18.5mg/mL 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 30% PEG3350, 10% glycerol, 200mM ammonium acetate, 100mM sodium acetate pH=5.0.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
Reflection twinOperator: l,-k,h / Fraction: 0.23
ReflectionResolution: 2→47.59 Å / Num. obs: 41204 / % possible obs: 99.5 % / Redundancy: 5.1 % / CC1/2: 0.994 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.05 / Net I/σ(I): 10.5 / Num. measured all: 210953 / Scaling rejects: 16
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
2-2.055.20.533.21575030310.8280.25399.8
8.94-47.594.90.06219.622124480.9910.0392.8

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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: 4YX5, 2LZM

4yx5

2lzm


Resolution: 2.0007→47.59 Å / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.03 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2096 1428 3.47 %
Rwork0.1571 39732 -
obs0.1586 41183 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 134.22 Å2 / Biso mean: 33.8494 Å2 / Biso min: 9.54 Å2
Refinement stepCycle: final / Resolution: 2.0007→47.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5104 0 0 657 5761
Biso mean---39.63 -
Num. residues----654
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085192
X-RAY DIFFRACTIONf_angle_d1.1597022
X-RAY DIFFRACTIONf_chiral_restr0.04814
X-RAY DIFFRACTIONf_plane_restr0.004896
X-RAY DIFFRACTIONf_dihedral_angle_d15.0241937
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0007-2.07220.24071220.22253989411197
2.0722-2.15510.25141460.21363960410696
2.1551-2.25320.2261540.20793947410196
2.2532-2.3720.23771350.19913985412096
2.372-2.52060.23361420.20283981412396
2.5206-2.71520.22251430.18833997414096
2.7152-2.98840.25021470.17373937408496
2.9884-3.42070.21951370.1433982411996
3.4207-4.30930.19781430.11123956409995
4.3093-47.6050.1591550.12053998415395
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.16533.01532.65342.97482.45522.0509-0.01430.7755-0.2088-0.15150.201-1.0614-1.39132.1126-0.3110.4797-0.2283-0.02070.54960.01280.45368.418934.781666.8944
20.7524-0.13090.80071.617-0.25555.3335-0.29230.491-0.2838-0.16150.1685-0.1479-0.05460.89520.01520.1404-0.07410.03010.3258-0.05340.21-3.464223.300252.4044
35.5918-1.3999-0.87051.76851.31690.9942-0.02560.67370.1847-0.55770.1931-0.3332-0.28380.22-0.10720.2688-0.11560.04730.2868-0.07360.1897-10.668924.794143.1459
47.27153.9126-1.70858.5883-1.06774.68280.05680.1877-0.44830.4447-0.1166-0.28320.28250.36680.07090.22010.0064-0.04180.2695-0.00750.1275-1.330320.504162.7297
59.9414.9927-0.14264.64811.74016.88370.4641-0.9023-0.66590.2483-0.2297-0.87030.65430.56-0.1090.395-0.1404-0.12480.61480.23790.68236.862319.054467.1088
61.53461.1691-1.63624.6385-4.19144.0464-0.13320.5455-0.3261-0.49320.0877-0.39520.15240.27010.03260.2029-0.08940.04670.3192-0.06330.1663-2.653624.720547.413
74.77763.76385.52163.75024.10946.34690.4277-0.87740.53730.8952-0.76290.35270.2693-0.14280.32370.3136-0.11550.00820.31280.00110.2244-3.672630.313665.4763
83.62413.6161-1.67819.47612.0773.23810.7618-0.5518-0.03720.22160.2537-0.23070.370.2803-0.88770.44020.1187-0.03070.63130.00730.37083.571326.754173.6113
93.43110.2656-0.7844.03010.07332.78480.0894-0.6563-0.18210.4222-0.0614-0.3584-0.0788-0.41540.14940.5520.0289-0.01980.63710.02770.1665-7.947522.839871.4477
106.91752.0598-2.92363.9958-2.50034.94970.16010.29740.25350.4373-0.2495-0.0788-0.15660.2090.1330.1891-0.05680.01380.23490.00010.1138-8.798928.611554.8682
113.77545.8775-2.70429.6064-3.90213.17240.0769-0.0697-0.23940.0342-0.2599-0.2772-0.00020.02580.08160.096-0.01530.02510.207-0.0430.1437-14.887424.704252.1399
122.79211.52480.04737.2232-2.48595.01250.02320.4621-0.515-0.17430.0775-0.01360.08420.0469-0.08520.0729-0.04150.0190.2104-0.09370.2233-15.588724.503449.037
134.9997-0.0466-2.73821.54010.67083.4304-0.27910.237-0.9487-0.13980.1436-0.07370.89270.02920.14290.3273-0.13750.01590.2974-0.05870.2818-20.709315.126450.2069
146.30862.6738-2.32462.1395-1.74042.8233-0.18150.7182-0.045-0.25780.21920.05240.1156-0.0734-0.0660.1814-0.0729-0.01180.2596-0.05050.1364-22.285821.667742.5903
152.56611.22320.21143.72853.28163.78570.3727-0.27540.363-0.2471-0.30150.1892-0.6844-0.2463-0.0870.15980.02140.00580.1581-0.00360.1642-34.075217.129860.6987
164.5524-0.616-0.86073.2242-0.09467.98090.3831-0.64910.16750.3048-0.17640.55270.7003-0.4671-0.14920.3868-0.05340.03490.3373-0.03150.2114-40.699116.618675.1272
176.79190.6236-5.4480.8524-1.15734.93440.1661-0.7623-0.338-0.0862-0.4427-0.06840.43010.1695-0.02330.4865-0.10550.03130.9014-0.30780.31-34.579120.146183.427
186.0877-0.41812.75171.2387-0.57371.36990.1981-1.29690.2971.4626-0.3070.77810.3727-0.45360.27831.03650.0570.36030.3123-0.27280.439-33.431727.751579.6153
192.6414-1.3145-0.36626.88052.77052.1751-0.374-0.62370.22461.09320.6118-0.6092-0.12850.3493-0.18290.31240.0066-0.06370.366-0.03350.1505-25.46214.447469.6991
201.5576-1.220.2693.490.15452.8952-0.1935-0.1916-0.270.08950.0418-0.271-0.01750.27970.1380.0816-0.00360.00360.13460.01890.1953-26.64593.608260.4756
215.0884-0.7795-3.61185.85540.67195.0298-0.0831-0.0501-0.31-0.0786-0.0423-0.37240.16210.14790.07940.07040.01030.01040.10310.01980.1686-29.6468-4.551557.9964
223.79110.1768-1.52063.15561.67927.02250.04850.22030.03660.1133-0.07780.17020.6927-0.7680.16110.1442-0.0040.00110.12070.01690.2287-39.6733-1.385755.2954
233.13230.3897-1.97263.2842-0.76864.1553-0.2163-0.114-0.015-0.25860.11130.2046-0.03610.0090.12580.1156-0.0037-0.05080.0793-0.00450.1548-36.22319.475352.3991
244.33770.7264-4.29674.74143.5538.19020.4189-1.1018-0.67140.9280.3878-0.51781.07130.7885-0.73770.29640.0584-0.05180.39060.04820.369213.597531.467457.4739
256.6079-1.22822.63512.2429-0.45223.7503-0.0748-0.2481-0.5731-0.10420.19130.1745-0.2218-0.5755-0.10730.13440.00880.02790.28320.06740.17010.888644.545441.9858
264.04611.5065-1.85344.12170.02221.1229-0.23550.3144-0.2118-0.1304-0.04630.680.2724-0.7303-0.01260.2368-0.44830.03490.87880.01970.4995-9.355337.651233.0424
274.84070.70541.99516.4786.08598.49790.2624-0.0298-0.04570.0971-0.1826-0.15170.1933-0.8540.00840.1761-0.0175-0.00190.17810.08550.13030.960446.000533.4862
286.0380.7652-1.71333.3542-0.72946.5767-0.011-0.17620.54880.21110.0241-0.1591-0.5155-0.1956-0.09430.12770.0281-0.06480.16260.02870.361310.186146.6448.9337
295.34833.0285-5.15584.1688-3.18755.19760.4857-1.007-0.26531.1367-0.7251-0.075-0.8535-0.13130.14670.3568-0.0909-0.02160.43470.00770.396513.301348.482254.9476
302.8126-0.49083.03481.54510.02713.76460.2121-0.3535-0.2323-0.06410.01530.11070.1314-0.3029-0.23990.1384-0.03120.00410.22260.08090.19876.38840.213944.1633
317.2815.4995-4.53214.4382-3.96663.8532-0.0237-0.73030.47670.46150.21650.1394-0.48640.0796-0.25510.26720.0087-0.07640.3369-0.08520.307518.0742.327757.8675
326.51291.11655.04322.87661.30485.23260.18310.08750.2660.0337-0.1213-0.16220.21480.35780.00980.1591-0.00480.00540.19290.04410.27113.738641.939841.0948
337.69725.4233-7.01434.9219-5.8667.31270.11870.0192-0.213-0.2782-0.30860.110.1685-0.08340.1160.17-0.0476-0.06970.24310.01170.12636.096242.438832.6655
348.05461.7592-0.73223.2290.79538.76680.01010.1708-0.1684-0.45890.1712-0.24410.404-0.1967-0.19160.1378-0.0099-0.02330.25510.05020.10274.538343.291729.9946
352.77712.33110.58872.16350.6032.0935-0.13940.1022-0.7022-0.20420.1025-0.4715-0.11560.1801-0.00120.20460.02590.07040.17850.0810.29921.508850.343221.1234
364.27710.90230.40422.7583-0.8661.6213-0.0795-0.42020.00940.0901-0.09-0.3458-0.10410.15150.10820.20860.0137-0.01050.15590.00520.147820.907662.502820.5635
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 11 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 12 through 22 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 23 through 40 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 41 through 63 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 64 through 69 )A0
6X-RAY DIFFRACTION6chain 'B' and (resid 3 through 10 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 11 through 17 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 18 through 24 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 25 through 35 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 36 through 47 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 48 through 57 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 58 through 69 )B0
13X-RAY DIFFRACTION13chain 'C' and (resid 1 through 17 )C0
14X-RAY DIFFRACTION14chain 'C' and (resid 18 through 35 )C0
15X-RAY DIFFRACTION15chain 'C' and (resid 36 through 44 )C0
16X-RAY DIFFRACTION16chain 'C' and (resid 45 through 71 )C0
17X-RAY DIFFRACTION17chain 'C' and (resid 72 through 83 )C0
18X-RAY DIFFRACTION18chain 'C' and (resid 84 through 92 )C0
19X-RAY DIFFRACTION19chain 'C' and (resid 93 through 113 )C0
20X-RAY DIFFRACTION20chain 'C' and (resid 114 through 139 )C0
21X-RAY DIFFRACTION21chain 'C' and (resid 140 through 158 )C0
22X-RAY DIFFRACTION22chain 'C' and (resid 159 through 175 )C0
23X-RAY DIFFRACTION23chain 'C' and (resid 176 through 196 )C0
24X-RAY DIFFRACTION24chain 'D' and (resid 5 through 11 )D0
25X-RAY DIFFRACTION25chain 'D' and (resid 12 through 22 )D0
26X-RAY DIFFRACTION26chain 'D' and (resid 23 through 28 )D0
27X-RAY DIFFRACTION27chain 'D' and (resid 29 through 42 )D0
28X-RAY DIFFRACTION28chain 'D' and (resid 43 through 60 )D0
29X-RAY DIFFRACTION29chain 'D' and (resid 61 through 69 )D0
30X-RAY DIFFRACTION30chain 'E' and (resid 4 through 17 )E0
31X-RAY DIFFRACTION31chain 'E' and (resid 18 through 26 )E0
32X-RAY DIFFRACTION32chain 'E' and (resid 27 through 46 )E0
33X-RAY DIFFRACTION33chain 'E' and (resid 47 through 57 )E0
34X-RAY DIFFRACTION34chain 'E' and (resid 58 through 69 )E0
35X-RAY DIFFRACTION35chain 'F' and (resid 1 through 83 )F0
36X-RAY DIFFRACTION36chain 'F' and (resid 84 through 195 )F0

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