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- PDB-4yxb: FliM(SPOA)::FliN fusion protein -

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Basic information

Entry
Database: PDB / ID: 4yxb
TitleFliM(SPOA)::FliN fusion protein
Components
  • (FliM::FliN fragment) x 2
  • Ambiguous peptide density
  • 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 / chemotaxis / 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 / Type III flagellar switch regulator (C-ring) FliN C-term
Similarity search - Domain/homology
IMIDAZOLE / : / Flagellar motor switch protein FliM / Flagellar motor switch protein FliN
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Salmonella enterica subsp. enterica serovar Typhimurium str. 798 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.56 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_assembly ...entity_src_gen / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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 motor switch protein FliM,Flagellar motor switch protein FliN
B: Flagellar motor switch protein FliM,Flagellar motor switch protein FliN
C: FliM::FliN fragment
D: FliM::FliN fragment
E: Ambiguous peptide density
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3726
Polymers60,3035
Non-polymers691
Water41423
1
A: Flagellar motor switch protein FliM,Flagellar motor switch protein FliN
B: Flagellar motor switch protein FliM,Flagellar motor switch protein FliN
C: FliM::FliN fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9324
Polymers50,8633
Non-polymers691
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-22 kcal/mol
Surface area17650 Å2
MethodPISA
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D: FliM::FliN fragment


  • defined by software
  • 8.91 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)8,9121
Polymers8,9121
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area1070 Å2
MethodPISA
3
E: Ambiguous peptide density


  • defined by software
  • 529 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)5291
Polymers5291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.150, 81.500, 89.960
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 3 molecules ABD

#1: Protein Flagellar motor switch protein FliM,Flagellar motor switch protein FliN


Mass: 25085.904 Da / Num. of mol.: 2
Fragment: UNP Residues 245-334,UNP Residues 5-137,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: Protein FliM::FliN fragment


Mass: 8911.981 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. 798 (bacteria), (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Gene: fliN, UMN798_2086, fliN, flaN, motD, STM1977 / Strain: LT2 / SGSC1412 / ATCC 700720 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0B4JZM9, UniProt: P26419

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Protein/peptide , 2 types, 2 molecules CE

#2: Protein/peptide FliM::FliN fragment


Mass: 690.787 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: P26419*PLUS
#4: Protein/peptide Ambiguous peptide density


Mass: 528.644 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: This peptide fragment was built into a region of electron density for which the sequence could not be definitively determined.
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Production host: Escherichia coli (E. coli)

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Non-polymers , 2 types, 24 molecules

#5: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.28 Å3/Da / Density % sol: 46.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: FliM(245-334)::FliN(5-137) was concentrated to 7.5mg/mL and crystallized with 2.2M NaCl, 100mM imidazole.Cl pH=8.0. Crystals were cryoprotected with 2M NaCl, 100mM imidazole.Cl pH=8.0, 30% glycerol.

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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: Sep 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.56→57.67 Å / Num. obs: 18420 / % possible obs: 100 % / Redundancy: 13.8 % / Biso Wilson estimate: 66.34 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.027 / Net I/σ(I): 18.5 / Num. measured all: 254307 / Scaling rejects: 12
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
2.56-2.6714.31.2152.73174022120.8140.332100
8.87-57.6712.10.05847.261865110.9980.01798.7

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Processing

Software
NameVersionClassification
Aimless0.2.7data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.56→47.078 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.47 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2593 1838 10 %
Rwork0.2175 16534 -
obs0.2218 18372 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 131.14 Å2 / Biso mean: 68.1747 Å2 / Biso min: 11.58 Å2
Refinement stepCycle: final / Resolution: 2.56→47.078 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2595 0 5 23 2623
Biso mean--73.44 64.45 -
Num. residues----354
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012642
X-RAY DIFFRACTIONf_angle_d1.3073608
X-RAY DIFFRACTIONf_chiral_restr0.045467
X-RAY DIFFRACTIONf_plane_restr0.005456
X-RAY DIFFRACTIONf_dihedral_angle_d14.71948
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 (%)
2.56-2.62920.41481480.311612291377100
2.6292-2.70660.3571360.307112621398100
2.7066-2.79390.38171470.289612481395100
2.7939-2.89380.33791300.287512611391100
2.8938-3.00960.31871460.270912531399100
3.0096-3.14650.33861450.25312371382100
3.1465-3.31240.27031190.234712741393100
3.3124-3.51990.2931490.225712571406100
3.5199-3.79150.28121480.22712711419100
3.7915-4.17290.22781320.192812841416100
4.1729-4.77620.18791460.161612821428100
4.7762-6.01550.23221420.208613001442100
6.0155-47.08640.24421500.21471376152699

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