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- PDB-6n74: Crystal Structure of ATPase delta1-79 Spa47 R271E -

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Basic information

Entry
Database: PDB / ID: 6n74
TitleCrystal Structure of ATPase delta1-79 Spa47 R271E
ComponentsATP synthase SpaL/MxiB
KeywordsBIOSYNTHETIC PROTEIN / ATPase
Function / homology
Function and homology information


protein-exporting ATPase activity / protein-secreting ATPase / type III protein secretion system complex / protein secretion by the type III secretion system / proton-transporting ATP synthase activity, rotational mechanism / ATP hydrolysis activity / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
ATPase, type III secretion system, FliI/YscN / T3SS EscN ATPase, C-terminal / T3SS EscN ATPase C-terminal domain / : / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain ...ATPase, type III secretion system, FliI/YscN / T3SS EscN ATPase, C-terminal / T3SS EscN ATPase C-terminal domain / : / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Type 3 secretion system ATPase
Similarity search - Component
Biological speciesShigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.852 Å
AuthorsMorales, Y. / Johnson, S.J. / Demler, H.J. / Dickenson, N.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R15AI124108-01A1 United States
CitationJournal: Proteins / Year: 2019
Title: Interfacial amino acids support Spa47 oligomerization and shigella type three secretion system activation.
Authors: Demler, H.J. / Case, H.B. / Morales, Y. / Bernard, A.R. / Johnson, S.J. / Dickenson, N.E.
History
DepositionNov 27, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 23, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP synthase SpaL/MxiB
B: ATP synthase SpaL/MxiB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,3854
Polymers78,1932
Non-polymers1922
Water7,584421
1
A: ATP synthase SpaL/MxiB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1922
Polymers39,0961
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ATP synthase SpaL/MxiB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1922
Polymers39,0961
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.153, 153.770, 54.706
Angle α, β, γ (deg.)90.000, 110.050, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ATP synthase SpaL/MxiB


Mass: 39096.379 Da / Num. of mol.: 2 / Mutation: delta 1-79, R271E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: spaL, mxiB, spa47, CP0149 / Plasmid: pTYB21 / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner(DE3)
References: UniProt: P0A1C1, H+-transporting two-sector ATPase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 421 / 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: 2.23 Å3/Da / Density % sol: 44.87 % / Mosaicity: 0.609 °
Crystal growTemperature: 298 K / Method: evaporation / pH: 8.5
Details: Tris, Ammonium Acetate, Lithium Sulfate, PEG 4000, MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 5, 2018
Details: Rh coated flat bent mirror , toroidal focusing post monochromator
RadiationMonochromator: Si(111) and Si(220) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 57246 / % possible obs: 99 % / Redundancy: 6.9 % / Biso Wilson estimate: 32.19 Å2 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.037 / Rrim(I) all: 0.099 / Χ2: 0.557 / Net I/σ(I): 3.7 / Num. measured all: 394559
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.85-1.926.81.23957150.5470.511.3430.43198.9
1.92-1.9970.84957030.7390.3430.9170.45599.1
1.99-2.086.80.57357060.8680.2340.620.46699
2.08-2.196.40.39156830.920.1650.4260.50297.9
2.19-2.337.10.28257110.9570.1140.3050.53499.5
2.33-2.517.10.20857170.9760.0840.2250.54399.3
2.51-2.766.80.14257390.9870.0580.1540.58898.9
2.76-3.1670.09457410.9940.0380.1010.67199.2
3.16-3.9970.06357530.9970.0260.0680.73499.2
3.99-5070.04857780.9980.0190.0520.62998.7

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementStarting model: 5SWJ

5swj


Resolution: 1.852→42.726 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.13
RfactorNum. reflection% reflection
Rfree0.2081 1993 3.48 %
Rwork0.1733 --
obs0.1745 57190 98.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 135.72 Å2 / Biso mean: 43.8183 Å2 / Biso min: 19.67 Å2
Refinement stepCycle: final / Resolution: 1.852→42.726 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5203 0 10 421 5634
Biso mean--93.51 46.22 -
Num. residues----665
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8525-1.89880.34631390.29233721386094
1.8988-1.95010.32041380.25833974411299
1.9501-2.00750.27551430.23383958410199
2.0075-2.07230.23581380.21493926406499
2.0723-2.14640.25191460.20373909405599
2.1464-2.23230.22641460.18023930407698
2.2323-2.33390.20981420.177939914133100
2.3339-2.45690.23251490.18683982413199
2.4569-2.61080.2291410.18343976411799
2.6108-2.81240.24191330.18613911404499
2.8124-3.09530.23341410.18453969411099
3.0953-3.5430.18821440.16773987413199
3.543-4.46310.17811500.14333945409598
4.4631-42.73720.17341430.15064018416199
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)
11.324-0.29370.34721.8179-0.78851.3832-0.0296-0.1518-0.01620.3071-0.0069-0.0588-0.23730.15080.07680.2708-0.043-0.01740.24590.02570.213964.18318.5828-14.5906
21.953-0.12350.38842.2209-0.30132.2225-0.1671-0.19440.33330.4222-0.0833-0.1493-0.56690.10330.08340.3939-0.0514-0.10540.2450.03470.285169.982325.0503-12.8948
31.4479-1.57610.55672.673-0.54840.2351-0.02960.0330.1650.168-0.03290.2247-0.1248-0.113-0.00690.24270.00370.01380.25310.00810.27749.571535.6241-31.241
43.44190.1316-0.11252.3104-0.35651.76490.09660.1630.2955-0.4150.01590.012-0.0942-0.03660.0850.41860.04320.04960.3940.08360.292265.48884.3342-51.7787
51.6062-0.1864-0.3391.7067-0.71631.4546-0.04190.1136-0.0555-0.21940.02320.01960.20310.09340.03420.25060.00430.01430.22680.03110.217959.8759-7.2816-32.5896
62.1996-0.48130.04841.2735-1.30991.3912-0.23520.637-0.6334-0.5784-0.05550.97940.5868-0.15320.07330.4416-0.0595-0.08030.4375-0.09730.500855.0482-6.3364-48.4693
72.0306-0.2372-0.16192.8433-0.76551.7977-0.00230.279-0.1765-0.6321-0.09360.03170.32390.18950.09130.36730.01560.03760.29810.04720.215664.7716-4.2564-47.8422
81.3337-0.61910.28313.84680.49871.85330.11530.2187-0.2285-0.818-0.45060.06830.39040.05160.00260.44420.06420.12980.27940.06490.281467.2521-11.985-43.9487
91.8328-0.2524-0.31932.28490.04312.3209-0.1624-0.0149-0.5786-0.14440.0654-0.13490.52050.15480.0440.32750.03790.09180.24320.06630.38466.8338-14.8195-35.8923
102.6402-0.0578-0.31912.6923-0.4892.15160.02710.0392-0.3765-0.28610.01010.16740.3495-0.0912-0.04180.324-0.03680.01430.25040.05140.336653.7399-16.7343-28.4009
112.68783.17880.36818.77551.30471.29170.0426-0.118-0.48730.1116-0.082-0.410.09250.1267-0.09010.2481-0.0120.02250.34730.09760.346746.8667-19.8521-17.3225
121.2030.4834-0.4991.1321-0.2221.2016-0.11540.096-0.2356-0.1360.15890.27040.4832-0.0981-0.15730.2867-0.02350.00120.36690.05460.450236.5881-25.5192-17.433
132.2794-0.24490.79773.16320.08094.2753-0.0101-0.26480.1140.09880.07520.5468-0.0349-0.6614-0.09310.2099-0.01040.00320.30440.06030.356542.5524-6.4979-25.1442
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 83 through 202 )A83 - 202
2X-RAY DIFFRACTION2chain 'A' and (resid 203 through 322 )A203 - 322
3X-RAY DIFFRACTION3chain 'A' and (resid 323 through 430 )A323 - 430
4X-RAY DIFFRACTION4chain 'B' and (resid 83 through 118 )B83 - 118
5X-RAY DIFFRACTION5chain 'B' and (resid 119 through 175 )B119 - 175
6X-RAY DIFFRACTION6chain 'B' and (resid 176 through 202 )B176 - 202
7X-RAY DIFFRACTION7chain 'B' and (resid 203 through 239 )B203 - 239
8X-RAY DIFFRACTION8chain 'B' and (resid 240 through 263 )B240 - 263
9X-RAY DIFFRACTION9chain 'B' and (resid 264 through 322 )B264 - 322
10X-RAY DIFFRACTION10chain 'B' and (resid 323 through 357 )B323 - 357
11X-RAY DIFFRACTION11chain 'B' and (resid 358 through 382 )B358 - 382
12X-RAY DIFFRACTION12chain 'B' and (resid 383 through 408 )B383 - 408
13X-RAY DIFFRACTION13chain 'B' and (resid 409 through 430 )B409 - 430

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