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Basic information

Entry
Database: PDB / ID: 8arc
TitleHeterologous Complex of Aeromonas hydrophila Type III secretion substrate AscX with Photorhabdus luminescens subsp. laumondii LscY
Components
  • AscX
  • Type III secretion protein SctY
KeywordsCHAPERONE / Type III Secretion System / T3SS / SctX / SctY
Function / homologyType III secretion system YscX / Type III secretion system chaperone, YscY / Type III secretion system YscX (type_III_YscX) / Tetratricopeptide-like helical domain superfamily / cytoplasm / BROMIDE ION / AscX / Type III secretion protein SctY
Function and homology information
Biological speciesPhotorhabdus laumondii subsp. laumondii TTO1 (bacteria)
Aeromonas hydrophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGilzer, D. / Niemann, H.H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2023
Title: The type III secretion chaperone SctY may shield the hydrophobic export gate-binding C-terminus of its substrate SctX.
Authors: Gilzer, D. / Kowal, J.L. / Flottmann, F. / Niemann, H.H.
History
DepositionAug 16, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _pdbx_initial_refinement_model.accession_code

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Type III secretion protein SctY
B: AscX
C: Type III secretion protein SctY
D: AscX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,49810
Polymers44,0194
Non-polymers4796
Water32418
1
A: Type III secretion protein SctY
B: AscX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3296
Polymers22,0092
Non-polymers3204
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Type III secretion protein SctY
D: AscX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1694
Polymers22,0092
Non-polymers1602
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.590, 34.220, 99.600
Angle α, β, γ (deg.)90.000, 101.810, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid -1 through 24 or resid 26...
d_2ens_1(chain "C" and (resid -1 through 24 or resid 26...
d_1ens_2chain "B"
d_2ens_2(chain "D" and (resid 50 through 63 or resid 67 through 118))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1HISPROA1 - 26
d_12ens_1ARGARGA28 - 47
d_13ens_1ALAALAA49 - 97
d_14ens_1SERGLNA99 - 107
d_15ens_1BRBRB
d_21ens_1HISPROI1 - 26
d_22ens_1ARGARGI28 - 47
d_23ens_1ALAALAI49 - 97
d_24ens_1SERGLNI99 - 107
d_25ens_1BRBRJ
d_11ens_2ARGLEUG1 - 66
d_21ens_2ARGHISM1 - 14
d_22ens_2HISLEUM18 - 69

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.999929644166, -0.00626301040684, 0.0100737985856), (-0.00560855760386, 0.997951332379, 0.0637313289159), (-0.0104523106969, 0.0636703455655, -0.997916247135)34.2998444205, -1.28694988494, 49.0358378378
2given(-0.999998450175, 0.0017082590537, -0.000426026894616), (0.00167329071122, 0.997421463643, 0.0717469439197), (0.000547490735306, 0.0717461198577, -0.997422776228)34.7873288303, -1.78839994306, 48.8706321183

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Components

#1: Protein Type III secretion protein SctY


Mass: 13401.528 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus laumondii subsp. laumondii TTO1 (bacteria)
Gene: sctY, plu3762 / Plasmid: pACYCDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7N0W7
#2: Protein AscX


Mass: 8607.969 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-terminal residues GAM remain after TEV-cleavage of the N-terminal MBP-tag.
Source: (gene. exp.) Aeromonas hydrophila (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q699R5
#3: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Br
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.73 Å3/Da / Density % sol: 29 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: reservoir solution: 0.15 M KBr, 24-26%(w/v) PEG2000 monomethyl ester; protein: 5 mg/mL in 20 mM Tris pH 8, 150 mM NaCl, 2 mM TCEP; drop size: 0.66 uL protein + 0.33 uL reservoir

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9187 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9187 Å / Relative weight: 1
ReflectionResolution: 2.1→48.8 Å / Num. obs: 32409 / % possible obs: 94.8 % / Redundancy: 1.99 % / Biso Wilson estimate: 44.94 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.063 / Net I/σ(I): 8.64
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 2 % / Mean I/σ(I) obs: 1.23 / Num. unique obs: 2393 / CC1/2: 0.588 / Rrim(I) all: 1.295 / % possible all: 94.7

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Processing

Software
NameVersionClassification
XDS20210205data reduction
XSCALE20220220data scaling
PHASER2.8.3phasing
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7QIH

7qih


Resolution: 2.1→48.75 Å / SU ML: 0.2865 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.7251
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2862 1582 4.9 %
Rwork0.2286 30694 -
obs0.2313 32276 94.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.91 Å2
Refinement stepCycle: LAST / Resolution: 2.1→48.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2776 0 6 18 2800
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00152853
X-RAY DIFFRACTIONf_angle_d0.4373851
X-RAY DIFFRACTIONf_chiral_restr0.029428
X-RAY DIFFRACTIONf_plane_restr0.0025498
X-RAY DIFFRACTIONf_dihedral_angle_d11.86571092
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.80765896232
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS0.825954507966
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.170.42461380.35882768X-RAY DIFFRACTION93.83
2.17-2.250.3731570.32592804X-RAY DIFFRACTION95.64
2.25-2.340.31331460.31642836X-RAY DIFFRACTION95.98
2.34-2.440.38151550.29122895X-RAY DIFFRACTION95.97
2.44-2.570.27821450.26842771X-RAY DIFFRACTION95.42
2.57-2.730.2811390.2722836X-RAY DIFFRACTION96.22
2.73-2.940.28891450.25252842X-RAY DIFFRACTION96.64
2.94-3.240.32091480.24842858X-RAY DIFFRACTION95.43
3.24-3.710.27061370.22112722X-RAY DIFFRACTION92.29
3.71-4.670.24621380.18992649X-RAY DIFFRACTION90.49
4.67-48.750.26491340.18522713X-RAY DIFFRACTION90.76
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)
17.179440761542.658904246893.760121043170.9847311068861.392226310231.9693451824-0.18401492611-0.820423552919-1.10380047091.40530598849-0.2092739819340.05046878885960.916789277607-0.101897292474-0.7118609100860.8123953096740.213733627070.2258438297630.4778173487190.14625043570.52702189955825.3964732201-14.081673425822.4119138718
29.483928795113.10032907823-3.65373429653.98541246481-1.25091365469.9764550659-0.723399719012-1.76274143122-0.8641454532770.398591654517-0.198360534829-0.2087559256891.877492305790.2066410857371.575098446410.6796671705560.07748114435560.1919851904431.10849952487-0.04480312072970.39767225372537.3249781919-7.091462743817.49618696348
30.7642045846970.746190730967-0.4762089235141.104045086980.4518151204232.52414924462-0.308389543727-0.0700307866953-0.311833462216-0.031802077340.03958857352710.08206883715240.321039949247-0.892250703495-0.1665985234870.4351456381450.03910471898090.08779547508680.5423269274860.02456755335790.1853642106047.5060128524-5.5124711764731.7837020145
43.989614177941.715273775650.9635119819383.489458428280.4201444251656.95144618849-0.479717787558-0.1924769504090.261098247445-0.5323494172580.0835051140335-0.0818009872958-0.5547093462190.2616937103540.4200523516240.4680086927130.03903408996580.002403649621590.350760901661-0.01833133127570.20267280289317.70162353633.4573094237733.2474153029
53.147797277091.997776077021.646139078918.737770891430.277596809366.76954869986-0.250047936826-0.048875819520.134903574649-1.01563495751-0.0206132901313-0.887384658877-0.1228583258161.26766745381-0.1191839667520.5074566548590.04749814975960.01363233530970.780470464824-0.06708650445270.31102324040826.51481368088.896908610843.0065369944
67.5777353748-0.9491920636125.741707876916.19289065498-5.396876673767.95131022662-0.406078082034-1.84267162544-0.584535380310.943422502748-0.5214362435850.5708581206961.05468271258-1.314774482281.173879565790.8611133223690.01133760679410.1002012125190.994640538216-0.09937693910830.39328605043415.05595006842.126932766947.6491164088
77.67978810594-2.47053739370.826824080430.84899720087-0.1441005597870.7432095062520.264469328804-0.7766428814590.8819637539630.419215323898-0.113851059796-0.01523314547430.542804771898-0.40018727066-0.4501975986850.8284459116530.1299377693880.2550142603320.794004968746-0.04561760285140.399358547626-1.791958760272.8774015112436.847552747
89.53029935065-2.72543109228-6.407239857767.61828188701-0.8536110993488.18782761678-0.2798067760330.759538404486-1.16935007946-0.441557665091-0.1034346843950.3007392204811.11665322318-1.233520492490.3688532021620.883633159039-0.2200420108950.04726158375820.838325008085-0.02073858491880.5798418188512.28396624573-11.13733196826.7166896099
96.483541160180.624975325585-2.587494122632.43932400109-1.894436510017.34351241807-0.8920599795031.29815669596-0.350473233067-0.6994275141550.118949841078-0.09350884470731.335568236890.1284987147533.4253707970.624712071145-0.1930685478320.1144923203091.151920136830.2070571964510.419137502492-3.02777877833-7.7666077447241.0278604943
101.16950324280.181191963616-2.506038628343.31146174816-0.4605003010815.38286295674-0.2040248044090.484106797062-0.3299086346240.3026547715310.222503260079-0.153440950470.8470942779071.233699233190.3487931165550.436919647570.02583861090860.09709247107380.56011344649-0.02124195535960.25883956054927.3661711787-4.640264188616.9548193203
113.14849937722-1.245601299811.043113245690.67128606211-1.009318068956.11944227139-0.3808174588750.1485059998460.283724988980.2493914453670.1068164643950.0350348630108-0.809141231429-0.361229434253-0.1286238559920.472673223446-0.01925063301690.03097535550460.4517802013050.110772542650.15928051643616.89789539754.2040825578516.0774581498
124.19986172643-1.00620725989-1.14337656168.21506608854-4.165609968054.70705910393-0.214844431058-0.7889770419380.05476464741251.325679405370.2403436545340.756467512326-0.748802456854-1.73684098751-0.122694103190.7682446705980.078366424950.05902498994980.9874707426240.06153338986860.4196362673058.377438232099.991251896656.38533598206
130.767225766015-0.3478914922151.143374686478.16818042367.44210629369.61282437704-0.1633102552860.782473147262-0.103961978146-0.771712648118-0.37776741196-1.527697510890.3729743600820.5568550218722.876274698170.925269536128-0.1135100505490.1217662824311.188362534550.3256394863130.59742430210619.79895885183.965439624151.61851293588
147.343368673843.751437941096.977940104813.099553283723.485964410646.63589826578-1.32911594360.8230724336072.01559809156-0.4607562805440.2418420583050.0403378463871.311075860492.880698963830.9479928159550.899366895016-0.0625887624534-0.03312192871441.321256494780.2225899855260.68388448729130.7178566276.5098129511211.5701278313
156.936198990891.963001772374.710387889215.865287555063.348765446325.16269621830.467843739620.9011763034972.21517897063-0.04703844860060.141754665120.4297484498210.4127502198921.59296373231-0.09511438935170.958223609421-0.3664571988380.2948618543411.332313570750.05569145974230.80036686506642.16695774062.6120032931713.8845094441
167.002904634293.18174724064-3.805765719197.45646405802-0.0707956411217.50321631229-0.255565684063-1.53380769271-1.151374225310.3165460098010.358189662189-1.28361787048-1.691714319641.62315798150.08625730907020.8642563801420.1312657582310.1567780048791.05104748515-0.08722653981510.69528854845838.301134152-8.2157918938521.1452449119
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'D' and (resid 89 through 103 )DM89 - 10340 - 54
22chain 'D' and (resid 104 through 118 )DM104 - 11855 - 69
33chain 'A' and (resid -1 through 37 )AA-1 - 371 - 39
44chain 'A' and (resid 38 through 75 )AA38 - 7540 - 77
55chain 'A' and (resid 76 through 105 )AA76 - 10578 - 107
66chain 'B' and (resid 50 through 59 )BG50 - 591 - 10
77chain 'B' and (resid 60 through 71 )BG60 - 7111 - 19
88chain 'B' and (resid 72 through 104 )BG72 - 10420 - 52
99chain 'B' and (resid 105 through 118 )BG105 - 11853 - 66
1010chain 'C' and (resid -1 through 37 )CI-1 - 371 - 39
1111chain 'C' and (resid 38 through 75 )CI38 - 7540 - 77
1212chain 'C' and (resid 76 through 105 )CI76 - 10578 - 107
1313chain 'D' and (resid 50 through 59 )DM50 - 591 - 10
1414chain 'D' and (resid 60 through 66 )DM60 - 6611 - 17
1515chain 'D' and (resid 67 through 71 )DM67 - 7118 - 22
1616chain 'D' and (resid 72 through 88 )DM72 - 8823 - 39

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