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- PDB-4iwb: Novel Fold of FliC/FliS Fusion Protein -

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Basic information

Entry
Database: PDB / ID: 4iwb
TitleNovel Fold of FliC/FliS Fusion Protein
ComponentsFliC, FliS chimera
KeywordsMOTOR PROTEIN / novel fold
Function / homology
Function and homology information


bacterial-type flagellum / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / structural molecule activity / extracellular region / cytosol
Similarity search - Function
Flagellar protein FliS / Flagellar protein FliS / Flagellar protein FliS superfamily / Flagellar protein FliS / Flagellin, C-terminal domain, subdomain 2 / Flagellin, C-terminal domain / Bacterial flagellin C-terminal helical region / Flagellin / Flagellin, N-terminal domain / Bacterial flagellin N-terminal helical region ...Flagellar protein FliS / Flagellar protein FliS / Flagellar protein FliS superfamily / Flagellar protein FliS / Flagellin, C-terminal domain, subdomain 2 / Flagellin, C-terminal domain / Bacterial flagellin C-terminal helical region / Flagellin / Flagellin, N-terminal domain / Bacterial flagellin N-terminal helical region / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Flagellin / Flagellar protein FliS
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsFaham, S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Protein design by fusion: implications for protein structure prediction and evolution.
Authors: Skorupka, K. / Han, S.K. / Nam, H.J. / Kim, S. / Faham, S.
History
DepositionJan 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FliC, FliS chimera
B: FliC, FliS chimera


Theoretical massNumber of molelcules
Total (without water)38,5852
Polymers38,5852
Non-polymers00
Water2,900161
1
A: FliC, FliS chimera


Theoretical massNumber of molelcules
Total (without water)19,2921
Polymers19,2921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: FliC, FliS chimera


Theoretical massNumber of molelcules
Total (without water)19,2921
Polymers19,2921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.129, 66.157, 97.169
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein FliC, FliS chimera / flagellin


Mass: 19292.281 Da / Num. of mol.: 2 / Fragment: SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: aq_1998, flaA, fliC, fliS / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: O67803, UniProt: O67806
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsPROTEIN IS A CHIMERA OF FLAGELLAR PROTEINS FLIC (UNP RESIDUES 478-518) AND FLIS (UNP RESIDUES 5-124) ...PROTEIN IS A CHIMERA OF FLAGELLAR PROTEINS FLIC (UNP RESIDUES 478-518) AND FLIS (UNP RESIDUES 5-124) CONNECTED BY A GLYCINE LINKER.

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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: 2.55 Å3/Da / Density % sol: 51.69 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 38% PEG500 MME, 0.1 M sodium chloride, 0.1 M Tris-HCl, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD
RadiationMonochromator: Rosenbaum-Rock double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. all: 39366 / Num. obs: 39366 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 19.7
Reflection shellResolution: 1.75→1.79 Å / Redundancy: 4 % / Rmerge(I) obs: 0.441 / Num. unique all: 2344 / % possible all: 88.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→29.09 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.933 / SU B: 4.354 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23235 1970 5 %RANDOM
Rwork0.20889 ---
all0.21008 37342 --
obs0.21008 37342 96.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.27 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20 Å2
2---0.05 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.75→29.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2612 0 0 161 2773
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222698
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8831.9823642
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0555332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.35926.154130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.32815556
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.4871512
X-RAY DIFFRACTIONr_chiral_restr0.0690.2429
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021959
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.441.51635
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.91622656
X-RAY DIFFRACTIONr_scbond_it1.72231063
X-RAY DIFFRACTIONr_scangle_it3.0474.5984
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.793 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 119 -
Rwork0.22 2370 -
obs--84.2 %
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)
10.8741-0.1340.01470.7546-0.02751.7142-0.0339-0.0525-0.04090.02690.01520.0360.065-0.05360.01880.01820.00470.01260.00630.00380.0847-4.9859-25.06151.5912
21.8327-0.5013-0.27261.20570.16651.02130.03040.10340.0212-0.103-0.01860.0174-0.0601-0.0347-0.01180.0660.02590.00560.0195-0.00540.047.5994-21.9147-30.2962
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 166
2X-RAY DIFFRACTION2B2 - 166

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