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- PDB-3usy: Crystal structure of Flig (residue 116-343) from H. Pylori -

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Basic information

Entry
Database: PDB / ID: 3usy
TitleCrystal structure of Flig (residue 116-343) from H. Pylori
ComponentsFlagellar motor switch protein
KeywordsMOTOR PROTEIN / motor switch protein / flagellar motor
Function / homology
Function and homology information


bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / bacterial-type flagellum / cytoskeletal motor activity / bacterial-type flagellum-dependent cell motility / chemotaxis / plasma membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2020 / Flagellar motor switch protein FliG, alpha-alpha superhelical domain / Flagellar motor switch protein FliG / Flagellar motor switch protein FliG, alpha-helical / Flagellar motor switch protein FliG, C-terminal / Flagellar motor switch protein FliG, N-terminal domain / Flagellar motor switch protein FliG, middle domain / FliG C-terminal domain / FliG middle domain / FliG N-terminal domain ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2020 / Flagellar motor switch protein FliG, alpha-alpha superhelical domain / Flagellar motor switch protein FliG / Flagellar motor switch protein FliG, alpha-helical / Flagellar motor switch protein FliG, C-terminal / Flagellar motor switch protein FliG, N-terminal domain / Flagellar motor switch protein FliG, middle domain / FliG C-terminal domain / FliG middle domain / FliG N-terminal domain / Annexin V; domain 1 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Flagellar motor switch protein FliG
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.706 Å
AuthorsLam, K.H. / Au, S.W.N.
CitationJournal: Structure / Year: 2012
Title: Multiple conformations of the FliG C-terminal domain provide insight into flagellar motor switching
Authors: Lam, K.H. / Ip, W.S. / Lam, Y.W. / Chan, S.O. / Ling, T.K.W. / Au, S.W.N.
History
DepositionNov 24, 2011Deposition site: RCSB / Processing site: PDBJ
SupersessionDec 14, 2011ID: 3PL4
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Nov 8, 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 / 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

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Assembly

Deposited unit
A: Flagellar motor switch protein
B: Flagellar motor switch protein


Theoretical massNumber of molelcules
Total (without water)52,2402
Polymers52,2402
Non-polymers00
Water91951
1
A: Flagellar motor switch protein


Theoretical massNumber of molelcules
Total (without water)26,1201
Polymers26,1201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Flagellar motor switch protein


Theoretical massNumber of molelcules
Total (without water)26,1201
Polymers26,1201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Flagellar motor switch protein

A: Flagellar motor switch protein


Theoretical massNumber of molelcules
Total (without water)52,2402
Polymers52,2402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area4860 Å2
ΔGint-42 kcal/mol
Surface area25000 Å2
MethodPISA
4
B: Flagellar motor switch protein

B: Flagellar motor switch protein


Theoretical massNumber of molelcules
Total (without water)52,2402
Polymers52,2402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_756-x+2,y,-z+11
Buried area4980 Å2
ΔGint-47 kcal/mol
Surface area25080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.378, 102.564, 91.582
Angle α, β, γ (deg.)90.00, 114.69, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Flagellar motor switch protein / FliG


Mass: 26120.162 Da / Num. of mol.: 2 / Fragment: residues 116-343
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: HP_0352 / Plasmid: pGEX-6p-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O25119
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 3.49 Å3/Da / Density % sol: 64.73 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES, 10% PEG6000, 0.02M SPERMIDINE, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 17, 2010
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.7→29.2 Å / Num. obs: 19547

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LKV

1lkv


Resolution: 2.706→29.2 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.834 / SU ML: 0.85 / σ(F): 0.58 / Phase error: 24.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2383 999 5.11 %
Rwork0.1943 --
obs0.1966 19547 99.67 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.63 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso max: 142.86 Å2 / Biso mean: 57.5776 Å2 / Biso min: 22.11 Å2
Baniso -1Baniso -2Baniso -3
1--0.5416 Å20 Å20.6012 Å2
2--1.3644 Å2-0 Å2
3----0.8228 Å2
Refinement stepCycle: LAST / Resolution: 2.706→29.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3532 0 0 51 3583
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093572
X-RAY DIFFRACTIONf_angle_d1.0844802
X-RAY DIFFRACTIONf_chiral_restr0.068570
X-RAY DIFFRACTIONf_plane_restr0.004612
X-RAY DIFFRACTIONf_dihedral_angle_d17.3951378
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7064-2.84890.33741580.27632584274299
2.8489-3.02720.35121450.253426412786100
3.0272-3.26070.27521370.215526512788100
3.2607-3.58830.25421290.204426352764100
3.5883-4.10630.21921430.187626692812100
4.1063-5.16890.21131460.164426712817100
5.1689-29.20170.19791410.176926972838100
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)
14.26053.36971.13397.30361.434.89370.2439-0.10590.05340.3436-0.06730.0780.3909-0.025-0.19930.27340.08890.01090.28050.04640.236555.7027-48.14256.5043
26.102-1.96721.53357.5048-2.57635.86780.0374-0.28390.59650.18710.01010.3785-0.5094-0.5525-0.03370.3045-0.02150.06610.3626-0.04230.333419.8855-36.2142-3.4457
35.3825-1.38562.74344.1535-0.1794.61050.128-0.0999-0.01510.3756-0.0001-0.09920.14210.0397-0.11850.3101-0.00750.03280.2324-0.01810.261125.5813-17.950711.3677
43.0266-0.7193-0.99426.03670.54653.67640.02580.0195-0.0058-0.35770.14510.4912-0.2623-0.2816-0.22240.3155-0.0211-0.04160.29680.09440.361778.890213.639135.6843
5-0.81511.00550.07546.35490.98270.87990.1347-0.06440.14160.4014-0.2291-0.03310.0086-0.16530.01720.3056-0.0224-0.03080.4221-0.06710.472347.7709-7.257838.5641
65.7741.6172-1.41185.9251-0.10174.59070.10550.06760.2725-0.20560.057-0.3916-0.45880.3764-0.22980.3791-0.0114-0.07450.3274-0.1070.404351.6564-18.281528.5616
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 110:199)A110 - 199
2X-RAY DIFFRACTION2chain 'A' and (resseq 200:244)A200 - 244
3X-RAY DIFFRACTION3chain 'A' and (resseq 245:336)A245 - 336
4X-RAY DIFFRACTION4chain 'B' and (resseq 110:197)B110 - 197
5X-RAY DIFFRACTION5chain 'B' and (resseq 198:279)B198 - 279
6X-RAY DIFFRACTION6chain 'B' and (resseq 280:336)B280 - 336

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