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- PDB-6n6l: Crystal Structure of ATPase delta 1-79 Spa47 R189A R191A mutant -

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Basic information

Entry
Database: PDB / ID: 6n6l
TitleCrystal Structure of ATPase delta 1-79 Spa47 R189A R191A mutant
ComponentsATP synthase SpaL/MxiB
KeywordsTRANSLOCASE / 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 complex, catalytic core F(1) / 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 / ATPases associated with a variety of cellular activities ...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 / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsMorales, Y. / Johnson, S.J. / Demler, H.J. / Dickenson, N.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Research Resources (NIH/NCRR)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 26, 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.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)78,0974
Polymers77,9042
Non-polymers1922
Water4,071226
1
A: ATP synthase SpaL/MxiB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0482
Polymers38,9521
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ATP synthase SpaL/MxiB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0482
Polymers38,9521
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.528, 152.916, 54.731
Angle α, β, γ (deg.)90.000, 110.900, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ATP synthase SpaL/MxiB


Mass: 38952.227 Da / Num. of mol.: 2 / Mutation: delta 1-79, R189A, R191A
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.: 226 / 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: 2.28 Å3/Da / Density % sol: 46.16 % / Mosaicity: 0.768 °
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: BL14-1 / Wavelength: 1.195 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 14, 2017
Details: Rh coated flat bent collimating mirror , toroidal focusing mirror
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.195 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 35105 / % possible obs: 90.7 % / Redundancy: 6.7 % / Biso Wilson estimate: 34.71 Å2 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.047 / Rrim(I) all: 0.127 / Χ2: 1.236 / Net I/σ(I): 6.4 / Num. measured all: 236601
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.15-2.236.91.37432480.4550.5551.4851.10184.3
2.23-2.326.81.08332170.6250.4411.1721.18383.3
2.32-2.426.80.79632310.7550.3210.861.08683.6
2.42-2.556.70.61632520.8310.2490.6661.08684.7
2.55-2.716.50.40934110.9530.1660.4431.12388.1
2.71-2.926.30.26135610.9630.1060.2821.10592.1
2.92-3.216.30.1536900.9870.0620.1631.16995.2
3.21-3.686.40.08837360.9950.0370.0961.29897.2
3.68-4.636.90.05538460.9980.0230.061.50298.9
4.63-507.60.04439130.9990.0170.0471.53699.7

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5SWJ

5swj


Resolution: 2.15→35.845 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 25.08
RfactorNum. reflection% reflection
Rfree0.2271 1762 5.03 %
Rwork0.1861 --
obs0.1881 35055 89.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 130.11 Å2 / Biso mean: 47.6778 Å2 / Biso min: 17.23 Å2
Refinement stepCycle: final / Resolution: 2.15→35.845 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5414 0 0 226 5640
Biso mean---45.41 -
Num. residues----696
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.15-2.18650.29921110.2712209173
2.1865-2.25080.3271350.267239285
2.2508-2.32350.30221220.2618236683
2.3235-2.40650.30761240.2472237183
2.4065-2.50280.25831300.2361244085
2.5028-2.61670.25931260.2272246187
2.6167-2.75460.27051310.2167254890
2.7546-2.92710.27091400.2181261593
2.9271-3.1530.23961480.2064270695
3.153-3.47010.21111490.1803277197
3.4701-3.97160.20691440.159278498
3.9716-5.00170.16841470.14222866100
5.0017-35.8450.21531550.16252882100
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)
11.5416-0.42980.19061.9372-0.40182.06970.07-0.0925-0.0540.0305-0.01710.04430.04020.0275-0.07470.2316-0.0214-0.03870.23030.02680.255720.226417.8907-15.0614
21.980.01480.21413.25510.76472.7419-0.0575-0.10670.25710.03880.1111-0.1942-0.29950.25-0.02310.2272-0.0102-0.0480.25570.05250.245629.201423.8623-9.9382
33.0123-1.44020.44391.603-0.68771.937-0.0129-0.01180.46850.0477-0.0661-0.0799-0.4726-0.15370.1060.35060.0084-0.03560.23630.01240.31249.747233.9531-28.3242
46.95680.15322.03811.7346-2.00536.79220.00820.62570.6605-0.6113-0.219-0.15130.11280.27250.17610.45560.05070.08350.33950.12880.398121.3093.9323-51.9566
54.32421.1824-0.15092.59320.01351.60240.0227-0.0442-0.20790.2925-0.0553-0.03280.1282-0.04330.01110.4069-0.04030.06220.2010.03890.231616.1881-7.7423-32.5816
65.2593-2.697-1.42181.83581.18725.5711-0.31970.5575-0.7731-0.261-0.28851.3540.5271-0.75830.56790.4288-0.1589-0.01330.344-0.02390.523110.6307-6.0327-47.1263
72.8966-2.3736-0.94247.2560.8224.02470.19330.286-0.2338-0.5251-0.22920.01490.3656-0.08870.03370.2878-0.04860.05550.27410.03650.211221.7889-7.8972-46.4946
83.3451-4.1984-4.38935.87714.8126.579-0.593-0.0164-0.511.03140.4264-0.82771.51270.32340.22090.65270.04840.00140.46270.04430.731936.2331-18.9851-41.9566
94.45872.02890.97426.12911.13955.2757-0.0872-0.1098-1.2852-0.18060.1537-0.32840.8029-0.0015-0.03550.3953-0.01820.11870.28970.06020.554721.1582-15.5689-35.2696
105.45660.92970.56592.1368-1.17044.40030.232-0.0968-0.83560.4323-0.0260.12070.7157-0.3585-0.18640.5284-0.10120.12880.29690.03540.47289.8854-17.1169-28.3519
118.56517.41165.03166.87035.34884.86750.4486-0.2928-0.60630.6246-0.3559-0.74240.4251-0.0018-0.05440.6416-0.02920.18180.42060.08740.3973.4394-19.6321-17.0896
128.01552.2541-4.34510.7102-1.6916.93490.2553-0.0984-0.18220.24610.08640.35710.6339-0.2621-0.42890.5632-0.21280.06120.4056-0.040.4711-7.2973-25.8676-17.5042
134.75243.0264-1.21657.7937-5.08077.026-0.02-0.3589-0.34960.6056-0.07440.315-0.3813-0.65120.11610.3506-0.00350.16630.33640.02860.4733-1.6402-6.9096-25.1277
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 287 )A203 - 287
3X-RAY DIFFRACTION3chain 'A' and (resid 288 through 430 )A288 - 430
4X-RAY DIFFRACTION4chain 'B' and (resid 83 through 118 )B83 - 118
5X-RAY DIFFRACTION5chain 'B' and (resid 119 through 174 )B119 - 174
6X-RAY DIFFRACTION6chain 'B' and (resid 175 through 202 )B175 - 202
7X-RAY DIFFRACTION7chain 'B' and (resid 203 through 264 )B203 - 264
8X-RAY DIFFRACTION8chain 'B' and (resid 265 through 287 )B265 - 287
9X-RAY DIFFRACTION9chain 'B' and (resid 288 through 322 )B288 - 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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