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- PDB-4yxc: Complex of FliM(SPOA)::FliN fusion protein and FliH(APAR)::T4lyso... -

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Basic information

Entry
Database: PDB / ID: 4yxc
TitleComplex of FliM(SPOA)::FliN fusion protein and FliH(APAR)::T4lysozyme fusion protein
Components
  • Flagellar assembly protein H,Endolysin
  • Flagellar motor switch protein FliM,Flagellar motor switch protein FliN
KeywordsPROTEIN TRANSPORT / Type III Secretion System
Function / homology
Function and homology information


bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / positive chemotaxis / cytoskeletal motor activity / bacterial-type flagellum-dependent cell motility / viral release from host cell by cytolysis / peptidoglycan catabolic process / chemotaxis / cell wall macromolecule catabolic process / lysozyme ...bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / positive chemotaxis / cytoskeletal motor activity / bacterial-type flagellum-dependent cell motility / viral release from host cell by cytolysis / peptidoglycan catabolic process / chemotaxis / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / host cell cytoplasm / defense response to bacterium / plasma membrane
Similarity search - Function
Flagellar motor switch protein FliN, N-terminal / Flagellar motor switch protein FliN N-terminal / : / Flagellar motor switch FliN / Flagellar motor switch FliN/Type III secretion HrcQb / Flagellar motor switch protein FliM / Flagellar motor switch protein FliM / CheC-like superfamily / Flagellar motor switch protein FliN-like, C-terminal domain / SpoA-like superfamily ...Flagellar motor switch protein FliN, N-terminal / Flagellar motor switch protein FliN N-terminal / : / Flagellar motor switch FliN / Flagellar motor switch FliN/Type III secretion HrcQb / Flagellar motor switch protein FliM / Flagellar motor switch protein FliM / CheC-like superfamily / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Endolysin / Flagellar motor switch protein FliM / Flagellar motor switch protein FliN
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Enteritidis str. SE30663 (bacteria)
Enterobacteria phage T4 (virus)
Salmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 23, 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: Flagellar assembly protein H,Endolysin
B: Flagellar motor switch protein FliM,Flagellar motor switch protein FliN


Theoretical massNumber of molelcules
Total (without water)45,6992
Polymers45,6992
Non-polymers00
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-16 kcal/mol
Surface area19390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.210, 76.370, 119.350
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Flagellar assembly protein H,Endolysin / Lysis protein / Lysozyme / Muramidase


Mass: 20800.652 Da / Num. of mol.: 1 / Fragment: UNP Residues 1-18 / Mutation: D20N, C54T, C97A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Enteritidis str. SE30663 (bacteria), (gene. exp.) Enterobacteria phage T4 (virus)
Gene: fliH, SEE30663_21114 / Production host: Escherichia coli (E. coli) / References: UniProt: L5WUL9, UniProt: P00720, lysozyme
#2: Protein Flagellar motor switch protein FliM,Flagellar motor switch protein FliN


Mass: 24898.326 Da / Num. of mol.: 1 / Fragment: UNP Residues 245-334,UNP Residues 5-137
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: fliM, cheC2, fla AII, fla QII, STM1976, fliN, flaN, motD, STM1977
Production host: Escherichia coli (E. coli) / References: UniProt: P26418, UniProt: P26419
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.15 Å3/Da / Density % sol: 42.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: FliM(245-334)::FliN(5-137) + FliH(1-18)::T4 lysozyme was concentrated to 17mg/mL and crystallized with 11% PEG400, 100mM sodium potassium phosphate pH=6.5. Crystals were cryoprotected with ...Details: FliM(245-334)::FliN(5-137) + FliH(1-18)::T4 lysozyme was concentrated to 17mg/mL and crystallized with 11% PEG400, 100mM sodium potassium phosphate pH=6.5. Crystals were cryoprotected with 40% PEG400, 200mM sodium potassium phosphate pH=6.5.

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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: Sep 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.3→64.33 Å / Num. obs: 18223 / % possible obs: 99.8 % / Redundancy: 12.9 % / Biso Wilson estimate: 52.31 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.02 / Net I/σ(I): 20.2 / Num. measured all: 234350 / 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
2.3-2.3812.90.9232.62266217560.8110.2699.8
8.91-64.3311.20.03157.240813640.9990.0196.7

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Processing

Software
NameVersionClassification
Aimless0.2.7data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YXB and 2LZM

4yxb

2lzm


Resolution: 2.3→47.022 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.262 1818 10 %
Rwork0.1967 16356 -
obs0.2031 18174 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 169.81 Å2 / Biso mean: 69.5779 Å2 / Biso min: 28.71 Å2
Refinement stepCycle: final / Resolution: 2.3→47.022 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2668 0 0 71 2739
Biso mean---65.48 -
Num. residues----349
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092713
X-RAY DIFFRACTIONf_angle_d1.153697
X-RAY DIFFRACTIONf_chiral_restr0.05441
X-RAY DIFFRACTIONf_plane_restr0.006478
X-RAY DIFFRACTIONf_dihedral_angle_d14.686999
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.36220.38741370.275112321369100
2.3622-2.43170.35041380.26312431381100
2.4317-2.51020.30881370.250512301367100
2.5102-2.59990.31641360.225712261362100
2.5999-2.7040.29771390.22912501389100
2.704-2.8270.271390.225212431382100
2.827-2.97610.33431360.233312291365100
2.9761-3.16250.29941380.228712531391100
3.1625-3.40660.32071400.218612541394100
3.4066-3.74930.23491410.189612701411100
3.7493-4.29150.24561430.165612871430100
4.2915-5.40560.20741440.15312901434100
5.4056-47.03190.24211500.19781349149998
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)
13.1023.6606-4.39554.9179-6.52568.65070.72360.82531.8192-0.21910.70391.3995-0.3569-0.3526-1.3250.89190.2144-0.060.7023-0.10610.725936.909148.092910.8935
24.7595-0.94541.93743.6259-3.03527.1029-0.57550.038-0.53580.5281-0.40880.3955-1.69430.38270.40880.92810.39470.03581.0337-0.14880.481542.876231.20624.6036
36.5850.41081.0588.7261-4.14512.2920.42780.0385-1.0114-0.2435-0.0671-0.00680.66160.9717-0.33010.46890.0573-0.09790.60190.0030.58746.95515.385739.0936
43.4614-1.827-2.53867.63110.80322.6341-0.2192-0.1027-0.09442.31890.22051.56380.7884-0.40290.2830.7213-0.1210.10150.54890.13490.696535.337611.025146.4463
53.48173.0089-0.87265.4981-3.88647.68650.7384-0.1757-0.5582-0.2521-0.47721.51250.2528-1.8786-0.04440.4145-0.1525-0.0430.8435-0.08060.974627.968611.509939.9305
64.94093.42431.7212.9759-1.5336.88990.39420.1621-0.4446-1.0607-0.25480.68591.06880.1515-0.27070.56850.04360.00820.36030.00710.399138.360418.868132.434
72.2352-3.4429-2.35967.57061.18036.12471.0909-0.3497-0.68640.3074-1.002-0.0328-1.52450.51070.060.73-0.17330.05510.5136-0.04680.391145.60435.169437.8683
87.4313-3.47332.20152.9420.09981.94280.3955-1.01380.41411.2315-0.2992-0.5842-0.89280.6771-0.18490.8889-0.4535-0.06840.8385-0.04980.475347.050229.678747.825
96.58312.5231-0.60256.60590.59435.74850.4564-0.6104-0.70171.1308-0.6815-1.3290.29640.74540.45050.5582-0.1926-0.20880.89530.12450.602254.034921.479146.6656
104.9367-3.78273.95085.2442-2.48095.5411-0.3698-0.5331-0.03920.41730.3790.3345-0.3091-0.5244-0.1220.28970.010.09310.3801-0.02870.399438.530829.99746.4854
113.61850.62081.53054.99840.05495.3873-0.2504-0.2863-0.31270.3819-0.01550.56450.1237-0.2770.16920.3040.02870.10970.35550.03520.285648.876415.955416.1437
122.551-1.25191.52692.8846-0.23570.6396-0.419-0.01980.27650.5511-0.0518-0.8270.12220.18830.60910.69520.17750.2920.58980.08340.316844.10128.5492-3.2829
135.9833-1.54754.69986.7632-1.66617.3171-0.08150.3546-0.42580.3915-0.0618-0.8650.180.3710.26750.3383-0.00220.0410.272-0.01670.369147.065126.45937.3579
149.7977-5.4537-1.2813.79712.59596.27410.1854-1.3128-0.73220.3838-0.1043-1.11960.31570.2211-0.28660.53720.0544-0.04030.46620.06210.637656.039115.370218.5321
157.4463-3.59964.29097.8452-3.96017.5169-1.1665-0.54540.46710.80150.4437-1.0509-1.47850.61270.58120.46150.0518-0.03620.413-0.07640.411447.841332.52879.5735
1610.0951-0.4818-1.53557.77821.55133.7641-0.854-1.52980.36211.09840.33880.0766-0.36610.21750.48820.65340.2033-0.14460.4413-0.04250.395139.002836.81649.8784
175.9791.20580.2031.72491.237.8317-0.85882.2072-0.0609-1.39971.1766-2.0844-0.03232.15230.39530.619-0.26820.17620.7334-0.03730.683444.281234.1053-7.9662
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 10 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 11 through 23 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 24 through 32 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 33 through 45 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 46 through 80 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 81 through 101 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 102 through 113 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 114 through 163 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 164 through 184 )A0
10X-RAY DIFFRACTION10chain 'B' and (resid 17 through 51 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 52 through 90 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 91 through 150 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 151 through 163 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 164 through 178 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 179 through 193 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 194 through 215 )B0
17X-RAY DIFFRACTION17chain 'B' and (resid 216 through 227 )B0

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