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- PDB-5xrw: Crystal structure of flagellar motor switch complex from H. pylori -

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Basic information

Entry
Database: PDB / ID: 5xrw
TitleCrystal structure of flagellar motor switch complex from H. pylori
Components
  • FliN
  • FliY
KeywordsMOTOR PROTEIN / motor switch complex / C-ring
Function / homology
Function and homology information


bacterial-type flagellum basal body / cytoskeletal motor activity / bacterial-type flagellum-dependent cell motility / chemotaxis / membrane / plasma membrane
Similarity search - Function
Surface presentation of antigens (SPOA) / SpoA-like / Flagellar motor switch FliN / Flagellar motor switch FliN/Type III secretion HrcQb / Flagellar motor switch protein FliN-like, C-terminal domain / SpoA-like superfamily / Type III flagellar switch regulator (C-ring) FliN C-term / CheC-like superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Flagellar motor switch protein FliN / Flagellar motor switch protein FliN
Similarity search - Component
Biological speciesHelicobacter pylori 26695 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsXue, C. / Lam, K.H. / Au, S.W.N.
Funding support Hong Kong, China, 2items
OrganizationGrant numberCountry
Research Grants CouncilN_CUHK454/13 Hong Kong
NSFC31370713 China
CitationJournal: J.Biol.Chem. / Year: 2018
Title: Three SpoA-domain proteins interact in the creation of the flagellar type III secretion system inHelicobacter pylori.
Authors: Lam, K.H. / Xue, C. / Sun, K. / Zhang, H. / Lam, W.W.L. / Zhu, Z. / Ng, J.T.Y. / Sause, W.E. / Lertsethtakarn, P. / Lau, K.F. / Ottemann, K.M. / Au, S.W.N.
History
DepositionJun 10, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2018Group: Data collection / Category: reflns / Item: _reflns.number_obs
Revision 1.2Dec 25, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: FliN
B: FliN
C: FliY
D: FliY


Theoretical massNumber of molelcules
Total (without water)34,8544
Polymers34,8544
Non-polymers00
Water1,40578
1
A: FliN
C: FliY


Theoretical massNumber of molelcules
Total (without water)17,4272
Polymers17,4272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-31 kcal/mol
Surface area9110 Å2
MethodPISA
2
B: FliN
D: FliY


Theoretical massNumber of molelcules
Total (without water)17,4272
Polymers17,4272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-32 kcal/mol
Surface area9010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.210, 49.210, 52.370
Angle α, β, γ (deg.)69.340, 82.980, 76.010
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
12chain C
22chain D

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
11SERSERASNASNchain AAA44 - 1221 - 79
21SERSERASNASNchain BBB44 - 1221 - 79
12LEULEULYSLYSchain CCC209 - 2862 - 79
22PROPROLYSLYSchain DDD208 - 2861 - 79

NCS ensembles :
ID
1
2

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Components

#1: Protein FliN /


Mass: 8747.040 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori 26695 (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: O25306*PLUS
#2: Protein FliY


Mass: 8680.200 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori 26695 (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: O25674*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 3.23 Å3/Da / Density % sol: 61.96 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2M Sodium acetate, 0.1M Tris HCl pH 8.5 and 30% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→29.42 Å / Num. all: 25061 / Num. obs: 13192 / % possible obs: 87.3 % / Redundancy: 1.9 % / Biso Wilson estimate: 34.23 Å2 / Net I/σ(I): 6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata collection
Aimlessdata scaling
PHASERphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→25.374 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 2.09 / Phase error: 24.6
RfactorNum. reflection% reflection
Rfree0.2286 671 5.09 %
Rwork0.2026 --
obs0.204 13190 87.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 118.27 Å2 / Biso mean: 43.1804 Å2 / Biso min: 14.17 Å2
Refinement stepCycle: final / Resolution: 2.5→25.374 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2408 0 0 78 2486
Biso mean---47.47 -
Num. residues----315
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092425
X-RAY DIFFRACTIONf_angle_d1.2173269
X-RAY DIFFRACTIONf_chiral_restr0.053407
X-RAY DIFFRACTIONf_plane_restr0.005416
X-RAY DIFFRACTIONf_dihedral_angle_d13.844918
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A726X-RAY DIFFRACTION4.211TORSIONAL
12B726X-RAY DIFFRACTION4.211TORSIONAL
21C730X-RAY DIFFRACTION4.211TORSIONAL
22D730X-RAY DIFFRACTION4.211TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5001-2.6930.30041330.26092565269890
2.693-2.96360.29061400.25632532267289
2.9636-3.39160.27711290.23162521265088
3.3916-4.26970.20571410.18712454259586
4.2697-25.37530.17581280.16032447257585
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)
10.3622-0.0358-0.14850.1120.13260.1288-0.54060.2408-0.00290.29440.18690.19640.37280.0802-0.20170.2025-0.0132-0.04060.2170.00320.23-58.1468-12.5559-26.8053
20.21280.0758-0.07970.8056-0.24380.1604-0.564-0.13860.45970.0419-0.1196-0.0903-0.33790.1182-0.88870.2904-0.1696-0.27110.1019-0.01080.2857-45.9727-5.4624-12.4985
30.5187-0.14970.06420.387-0.66331.3710.02380.4004-0.00560.02-0.2574-0.53930.29120.3227-0.99460.20320.10060.09320.3669-0.06410.0629-50.8754-13.2132-30.4268
42.1858-0.01781.4440.6054-0.20471.1135-0.17530.76360.4351-0.046-0.07940.0124-0.32670.5095-0.10770.30480.02480.09350.26130.03710.2441-57.1436-11.7667-37.8886
50.2289-0.070.3641.20340.10661.0597-0.03560.7130.1714-0.2378-0.3806-0.1248-0.44840.3313-0.14260.2071-0.0522-0.04880.41420.04460.2812-57.7562-8.4708-40.8837
60.3450.02880.13810.0482-0.02530.0948-0.1884-0.1521-0.3460.07280.0839-0.3670.16510.0235-0.01050.30350.0137-0.06090.2844-0.11910.542-70.002-23.368-33.8229
70.376-0.0490.14940.244-0.20390.10970.2985-0.4339-0.22860.2103-0.3447-0.1802-0.02320.0058-0.00330.2701-0.0180.02660.25390.01820.1982-49.5895-38.419-40.9513
80.45590.07190.15820.03720.13690.51620.10390.0623-0.19590.10580.15960.30740.3468-0.00830.01470.2728-0.1418-0.01090.15970.05360.167-56.7534-48.0789-49.3914
90.5989-0.11140.19890.50030.11240.12660.237-0.23610.2560.4838-0.20590.0599-0.0652-0.16670.04510.15730.04710.11510.19770.03630.2003-51.4277-29.3168-44.284
100.52810.85650.05381.43230.22290.3708-0.22030.1091-0.0557-0.52250.4273-0.0012-0.00540.13850.01990.25830.0018-0.0150.27710.00740.3429-43.6411-23.8131-48.3811
110.53390.0950.61430.0692-0.0560.9608-0.0643-0.416-0.2215-0.2230.1022-0.0768-0.1247-0.23630.00610.223-0.04890.01660.2554-0.02780.1917-37.462-22.3674-42.3418
121.1580.1919-0.03620.42710.15691.0218-0.24410.019-0.07490.2281-0.2920.00580.2766-0.1062-1.29040.2954-0.0567-0.00910.26170.09280.0538-52.5524-13.7631-19.1783
130.2603-0.35580.04350.4797-0.08070.0088-0.5092-0.1437-0.18710.081-0.08750.32890.02980.0009-0.5333-0.06360.0498-0.23310.33790.0840.3634-66.3387-7.4463-33.637
140.53770.11840.59510.1341-0.35142.1528-0.10480.5036-0.03770.1351-0.43980.2715-0.53140.1749-0.19750.2480.0217-0.07170.25510.01160.3573-66.0079-11.267-41.3226
150.93090.00750.09260.13920.18970.9435-0.49450.0030.7243-0.14750.07760.0981-0.05330.1827-0.32390.2767-0.1641-0.02340.19840.04430.3446-55.8993-2.8524-25.8897
160.18050.03880.1991-0.00430.03960.18230.12670.25060.09540.09980.1207-0.1907-0.32210.22390.01210.3283-0.0351-0.01020.25680.02730.3093-50.2624-3.3023-23.8085
170.08930.0015-0.24630.5255-0.50311.1337-0.2740.17230.22670.1606-0.2326-0.3279-0.29690.4972-0.41570.12540.0354-0.07420.50130.04580.3144-45.5707-3.5975-24.8216
180.00920.0205-0.00640.5121-0.29650.2234-0.0384-0.1415-0.0310.1349-0.0983-0.049-0.1307-0.1306-0.53930.3480.6631-0.27120.78160.15290.1274-56.6817-4.3458-8.1905
190.1264-0.01430.28670.96920.74371.24170.5069-0.37080.21450.6882-0.0894-0.35220.4282-0.19020.48450.2554-0.03610.03340.1460.0370.2434-44.6521-35.446-41.8872
200.2577-0.02430.14990.45290.44410.3883-0.18760.07760.0154-0.18380.2081-0.14650.04250.10520.00870.2774-0.00430.03380.157-0.01010.1966-42.7871-32.3492-49.4446
210.1940.1846-0.23890.2047-0.20120.13860.09670.1409-0.02-0.1203-0.1195-0.17790.1701-0.1213-00.3016-0.0194-0.01160.1936-0.0620.2863-52.0081-46.4201-45.8361
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 44 through 58 )A44 - 58
2X-RAY DIFFRACTION2chain 'A' and (resid 59 through 69 )A59 - 69
3X-RAY DIFFRACTION3chain 'A' and (resid 70 through 87 )A70 - 87
4X-RAY DIFFRACTION4chain 'A' and (resid 88 through 98 )A88 - 98
5X-RAY DIFFRACTION5chain 'A' and (resid 99 through 109 )A99 - 109
6X-RAY DIFFRACTION6chain 'A' and (resid 110 through 122 )A110 - 122
7X-RAY DIFFRACTION7chain 'B' and (resid 44 through 64 )B44 - 64
8X-RAY DIFFRACTION8chain 'B' and (resid 65 through 69 )B65 - 69
9X-RAY DIFFRACTION9chain 'B' and (resid 70 through 87 )B70 - 87
10X-RAY DIFFRACTION10chain 'B' and (resid 88 through 98 )B88 - 98
11X-RAY DIFFRACTION11chain 'B' and (resid 99 through 122 )B99 - 122
12X-RAY DIFFRACTION12chain 'C' and (resid 209 through 217 )C209 - 217
13X-RAY DIFFRACTION13chain 'C' and (resid 218 through 224 )C218 - 224
14X-RAY DIFFRACTION14chain 'C' and (resid 225 through 240 )C225 - 240
15X-RAY DIFFRACTION15chain 'C' and (resid 241 through 253 )C241 - 253
16X-RAY DIFFRACTION16chain 'C' and (resid 254 through 264 )C254 - 264
17X-RAY DIFFRACTION17chain 'C' and (resid 265 through 275 )C265 - 275
18X-RAY DIFFRACTION18chain 'C' and (resid 276 through 286 )C276 - 286
19X-RAY DIFFRACTION19chain 'D' and (resid 208 through 224 )D208 - 224
20X-RAY DIFFRACTION20chain 'D' and (resid 225 through 264 )D225 - 264
21X-RAY DIFFRACTION21chain 'D' and (resid 265 through 286 )D265 - 286

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