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- PDB-6lea: Structure of FliS chaperone in complex with flagellin and HP1076 -

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Basic information

Entry
Database: PDB / ID: 6lea
TitleStructure of FliS chaperone in complex with flagellin and HP1076
Components
  • Flagellar secretion chaperone FliS
  • Flagellin
  • Uncharacterized protein HP_1076
KeywordsCHAPERONE / Flagellar / complex
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 FLiS export co-chaperone, HP1076 / Flagellar FLiS export co-chaperone, HP1076 / FLiS export co-chaperone, HP1076 superfamily / Flagellar FLiS export co-chaperone, HP1076 / Flagellar protein FliS / Flagellar protein FliS / Flagellar protein FliS superfamily / Flagellar protein FliS / Flagellin hook, IN motif / Flagellin hook IN motif ...Flagellar FLiS export co-chaperone, HP1076 / Flagellar FLiS export co-chaperone, HP1076 / FLiS export co-chaperone, HP1076 superfamily / Flagellar FLiS export co-chaperone, HP1076 / Flagellar protein FliS / Flagellar protein FliS / Flagellar protein FliS superfamily / Flagellar protein FliS / Flagellin hook, IN motif / Flagellin hook IN motif / Bacterial flagellin C-terminal helical region / Flagellin / Flagellin, N-terminal domain / Bacterial flagellin N-terminal helical region / Arylsulfatase, C-terminal domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Flagellin / Flagellar secretion chaperone FliS / Uncharacterized protein / Flagellin B
Similarity search - Component
Biological speciesHelicobacter pylori CPY1124 (bacteria)
Helicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsAu, S.W. / Lam, W.W.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC)14100114 Hong Kong
Citation
Journal: To Be Published
Title: Structure of FliS in complex with flagellin and HP1076
Authors: Lam, W.W. / Sun, K. / Au, S.W.
#1: Journal: FASEB J / Year: 2010
Title: Molecular interaction of flagellar export chaperone FliS and cochaperone HP1076 in Helicobacter pylori.
Authors: Lam, W.W. / Woo, E.J. / Kotaka, M. / Tam, W.K. / Leung, Y.C. / Ling, T.K. / Au, S.W.
History
DepositionNov 25, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Flagellar secretion chaperone FliS
B: Flagellar secretion chaperone FliS
C: Uncharacterized protein HP_1076
D: Uncharacterized protein HP_1076
E: Flagellin
F: Flagellin


Theoretical massNumber of molelcules
Total (without water)93,2786
Polymers93,2786
Non-polymers00
Water19811
1
A: Flagellar secretion chaperone FliS
C: Uncharacterized protein HP_1076
E: Flagellin


Theoretical massNumber of molelcules
Total (without water)46,6393
Polymers46,6393
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-39 kcal/mol
Surface area13960 Å2
MethodPISA
2
B: Flagellar secretion chaperone FliS
D: Uncharacterized protein HP_1076
F: Flagellin


Theoretical massNumber of molelcules
Total (without water)46,6393
Polymers46,6393
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-37 kcal/mol
Surface area13740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.330, 103.330, 144.211
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
12(chain C and resid 27 through 147)
22(chain D and resid 27 through 147)
13chain E
23chain F

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUSERSERchain AAA18 - 12223 - 127
21GLUGLUSERSERchain BBB18 - 12223 - 127
12SERSERSERSER(chain C and resid 27 through 147)CC27 - 14733 - 153
22SERSERSERSER(chain D and resid 27 through 147)DD27 - 14733 - 153
13VALVALGLNGLNchain EEE476 - 51467 - 105
23VALVALGLNGLNchain FFF476 - 51467 - 105

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Flagellar secretion chaperone FliS


Mass: 14969.931 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori CPY1124 (bacteria) / Gene: fliS, HPCPY1124_0918 / Production host: Escherichia coli (E. coli) / References: UniProt: I9NY49
#2: Protein Uncharacterized protein HP_1076


Mass: 20134.928 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (strain ATCC 700392 / 26695) (bacteria)
Gene: HP_1076 / Production host: Escherichia coli (E. coli) / References: UniProt: O25709
#3: Protein Flagellin


Mass: 11533.993 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: HPF63_0124 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Q2QRN0, UniProt: Q07911*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.38 Å3/Da / Density % sol: 48.38 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 3% (v/v) PEG 20000, 0.2M Potassium bromide, 0.2M Potassium thiocyanate, 0.2M Sodium acetate pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 25, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.95→40.62 Å / Num. obs: 16741 / % possible obs: 90.9 % / Redundancy: 9.7 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 16.6
Reflection shellResolution: 2.95→3.11 Å / Rmerge(I) obs: 0.452 / Num. unique obs: 2628

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Processing

Software
NameVersionClassification
PHENIX1.17rc1_3605refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K1I

3k1i


Resolution: 2.95→30.62 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 26.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2473 1611 10 %
Rwork0.1896 14502 -
obs0.1954 16113 87.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 162.71 Å2 / Biso mean: 61.7515 Å2 / Biso min: 25.4 Å2
Refinement stepCycle: final / Resolution: 2.95→30.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4272 0 0 11 4283
Biso mean---38.39 -
Num. residues----537
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A634X-RAY DIFFRACTION1.464TORSIONAL
12B634X-RAY DIFFRACTION1.464TORSIONAL
21C724X-RAY DIFFRACTION1.464TORSIONAL
22D724X-RAY DIFFRACTION1.464TORSIONAL
31E230X-RAY DIFFRACTION1.464TORSIONAL
32F230X-RAY DIFFRACTION1.464TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.95-3.040.32351370.25671265140291
3.04-3.130.34781360.25691267140393
3.13-3.250.31111390.2461280141994
3.25-3.380.35251480.2381295144394
3.38-3.530.32241020.225789199364
3.53-3.720.2783890.230274983855
3.72-3.950.328980.205886796564
3.95-4.250.25311480.16641362151098
4.25-4.680.19611520.150513831535100
4.68-5.350.1991530.15491360151399
5.35-6.730.21261510.202413851536100
6.73-30.620.19141580.16231398155699
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)
11.96281.27082.43372.45631.08443.2780.35150.7811-0.4445-0.5856-0.10020.1174-0.6291-0.1044-0.00140.37020.0303-0.00230.40590.07960.386437.5-30.027125.3576
21.5921.3996-1.81484.28031.90014.85870.5734-0.4118-1.4089-0.0538-0.25430.16440.1881-0.18750.00160.32280.0197-0.0090.30230.05640.414937.1481-33.476534.3621
30.30690.9017-0.2853.3286-0.49193.86670.2699-1.49820.14180.25480.0261-0.2143-0.1343-0.2112-0.00130.34610.0434-0.09310.4905-0.07160.352140.2874-25.892240.1796
42.05910.47112.35873.5991.14413.85780.51230.03821.2699-0.4290.1875-0.1354-0.74660.08740.00150.4544-0.03190.06090.36210.08470.45141.5961-22.176528.7493
53.91371.6285-0.35852.34670.26792.0034-0.4042-0.3343-0.34111.48480.78610.1434-0.3738-0.3725-0.00480.40310.01260.00560.4591-0.0310.354929.3703-37.952116.5657
63.69282.87212.0293.71910.24094.8975-0.46320.13320.27130.18190.8019-0.9631-0.75120.16450.01980.3947-0.05470.08140.4015-0.04280.406732.4962-31.58948.6865
70.5258-0.6359-0.72231.39630.05972.00110.69471.6461-2.1917-1.69290.139-1.66350.4882-0.22670.21070.7421-0.2095-0.0030.6656-0.37661.30532.7475-56.44523.5647
83.63931.63911.32164.0840.29992.6472-0.02360.3043-0.3147-0.27020.33290.43650.0961-0.06410.00180.4437-0.01120.04640.4817-0.08310.391723.2815-40.87827.8637
91.25350.9129-0.33050.84230.14620.65680.1124-0.8891-0.34110.08950.0154-0.03350.2009-0.1673-0.00030.41050.0059-0.02470.57180.01840.416926.876-33.828443.8041
103.59281.51461.90022.04360.00241.25220.2463-0.0359-0.9370.0018-0.14290.23250.0213-0.4053-0.00270.5331-0.0456-0.00930.7081-0.07020.55383.6056-34.365340.668
11-0.01070.06630.02870.82170.43510.17980.6101-0.927-0.2871-0.5534-0.9859-0.31840.58770.60660.00620.5886-0.1417-0.04130.94710.28540.757524.6619-33.864755.5177
120.2382-0.45780.27611.0496-0.59480.2914-0.4412-1.9088-0.7916-0.00750.93160.97110.5671-0.85320.01950.6454-0.1227-0.1311.05540.0760.57080.5233-36.355348.9384
130.1988-0.18250.66120.2189-0.27783.138-0.0697-2.18561.0820.088-0.16750.3384-0.3668-0.5912-0.00570.3791-0.01390.03770.7315-0.18120.615213.6468-26.654150.8725
141.23271.24260.35263.3295-0.83991.3313-0.3260.10610.0917-0.19680.34860.1394-0.3395-0.14890.00880.7217-0.1410.05130.6190.00250.361932.4273-11.32110.8017
151.60332.0605-0.14782.2638-0.51593.9533-0.27410.3243-0.0049-0.74870.44430.0283-0.8280.1036-0.00320.9515-0.2553-0.03140.6601-0.03130.480932.4959-14.5704-7.2921
160.2397-0.22540.37090.2712-0.24160.4654-0.9866-0.80311.58431.3861-1.2772-0.8734-1.4106-1.0513-0.01490.7858-0.0540.12710.7805-0.24311.026244.1065-17.203841.8872
170.76780.01711.66470.31450.01784.06320.59630.41630.5888-0.035-0.8251-0.3314-0.83921.4388-0.25730.7789-0.22140.04980.2601-0.15080.694849.1705-16.904231.6491
181.4701-2.7232-3.48415.36096.40058.21270.3546-1.1349-0.97752.082-0.6896-0.79140.64312.27790.06940.2001-0.52280.0040.8259-0.37531.0257.6177-22.911235.5133
190.18530.3439-0.84691.4137-2.76085.74970.21070.2741-0.65091.23620.6271-1.5461-1.15131.76490.24570.08630.081-0.12740.5618-0.1290.750553.1666-34.139630.5113
200.1929-0.0118-0.24970.2576-0.15640.23780.213-0.1702-0.42160.5239-0.4407-0.31450.866-0.71850.00140.40150.0273-0.05380.48930.05390.472140.1511-42.22325.7354
210.0217-0.0459-0.01970.1692-0.12410.4284-0.30090.3573-0.8474-0.5304-0.48660.1867-0.8782-0.9169-0.00130.7554-0.2518-0.1220.84380.04680.535816.6587-44.7445-1.1527
221.54481.9537-0.83782.7193-1.7792.57930.3616-0.05280.69490.74140.25951.8885-0.1611-1.79560.18120.4422-0.21380.02650.78680.07590.622314.9151-43.74137.3017
231.3968-0.99751.08281.7951-2.00532.31050.2381-0.3465-1.6121-0.3621-0.07640.12662.0166-0.30060.33560.4258-0.2471-0.03040.64440.0510.693419.0172-54.19018.9459
241.50381.1204-3.19640.8682-2.39976.8256-0.13171.3097-0.4596-0.56470.1955-1.09731.3869-0.86310.0750.53650.0943-0.12030.3423-0.22870.962333.3998-53.508911.1858
251.7521.54581.50192.39642.57322.9218-1.34790.31260.4107-0.92761.0378-0.3322-0.49591.70730.09320.37750.08060.13340.4696-0.0390.594541.5178-40.60115.9704
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 18 through 43 )A18 - 43
2X-RAY DIFFRACTION2chain 'A' and (resid 44 through 74 )A44 - 74
3X-RAY DIFFRACTION3chain 'A' and (resid 75 through 97 )A75 - 97
4X-RAY DIFFRACTION4chain 'A' and (resid 98 through 122 )A98 - 122
5X-RAY DIFFRACTION5chain 'B' and (resid 18 through 43 )B18 - 43
6X-RAY DIFFRACTION6chain 'B' and (resid 44 through 66 )B44 - 66
7X-RAY DIFFRACTION7chain 'B' and (resid 67 through 75 )B67 - 75
8X-RAY DIFFRACTION8chain 'B' and (resid 76 through 122 )B76 - 122
9X-RAY DIFFRACTION9chain 'C' and (resid 22 through 60 )C22 - 60
10X-RAY DIFFRACTION10chain 'C' and (resid 61 through 102 )C61 - 102
11X-RAY DIFFRACTION11chain 'C' and (resid 103 through 109 )C103 - 109
12X-RAY DIFFRACTION12chain 'C' and (resid 110 through 120 )C110 - 120
13X-RAY DIFFRACTION13chain 'C' and (resid 121 through 147 )C121 - 147
14X-RAY DIFFRACTION14chain 'D' and (resid 27 through 85 )D27 - 85
15X-RAY DIFFRACTION15chain 'D' and (resid 86 through 149 )D86 - 149
16X-RAY DIFFRACTION16chain 'E' and (resid 476 through 483 )E476 - 483
17X-RAY DIFFRACTION17chain 'E' and (resid 484 through 491 )E484 - 491
18X-RAY DIFFRACTION18chain 'E' and (resid 492 through 496 )E492 - 496
19X-RAY DIFFRACTION19chain 'E' and (resid 497 through 505 )E497 - 505
20X-RAY DIFFRACTION20chain 'E' and (resid 506 through 514 )E506 - 514
21X-RAY DIFFRACTION21chain 'F' and (resid 476 through 481 )F476 - 481
22X-RAY DIFFRACTION22chain 'F' and (resid 482 through 486 )F482 - 486
23X-RAY DIFFRACTION23chain 'F' and (resid 487 through 496 )F487 - 496
24X-RAY DIFFRACTION24chain 'F' and (resid 497 through 505 )F497 - 505
25X-RAY DIFFRACTION25chain 'F' and (resid 506 through 514 )F506 - 514

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