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- PDB-6n73: Crystal Structure of ATPase delta1-79 Spa47 R271A -

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Basic information

Entry
Database: PDB / ID: 6n73
TitleCrystal Structure of ATPase delta1-79 Spa47 R271A
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 / biosynthetic process / ATP metabolic process / proton transmembrane transport / 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: 2.398 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


Theoretical massNumber of molelcules
Total (without water)78,0772
Polymers78,0772
Non-polymers00
Water1,04558
1
A: ATP synthase SpaL/MxiB


Theoretical massNumber of molelcules
Total (without water)39,0381
Polymers39,0381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ATP synthase SpaL/MxiB


Theoretical massNumber of molelcules
Total (without water)39,0381
Polymers39,0381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.199, 154.117, 54.905
Angle α, β, γ (deg.)90.000, 110.030, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ATP synthase SpaL/MxiB


Mass: 39038.344 Da / Num. of mol.: 2 / Mutation: delta 1-79, R271A
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.25 Å3/Da / Density % sol: 45.34 % / Mosaicity: 0.762 °
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: 1.55 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 2, 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: 1.55 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 25991 / % possible obs: 96.4 % / Redundancy: 5.8 % / Biso Wilson estimate: 58.1 Å2 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.05 / Rrim(I) all: 0.123 / Χ2: 2.541 / Net I/σ(I): 7.7 / Num. measured all: 150622
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.494.50.65224300.7410.3260.7320.82490.6
2.49-2.595.70.57325260.8340.2540.6280.90694.5
2.59-2.76.30.44226140.8880.1890.4821.15197.7
2.7-2.856.20.34425860.9210.1490.3761.4996.7
2.85-3.025.90.26225920.9540.1160.2882.08595.4
3.02-3.266.20.19326290.9740.0840.2112.60797.9
3.26-3.5860.14526380.9830.0650.163.29898.1
3.58-4.15.60.10726330.990.0490.1184.03796.9
4.1-5.175.80.08726640.9930.0390.0954.1798.8
5.17-505.90.07926790.9950.0360.0874.30797.6

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Processing

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

5swj


Resolution: 2.398→32.295 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 26.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2354 1300 5.01 %
Rwork0.1849 24657 -
obs0.1874 25957 96.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 171.52 Å2 / Biso mean: 68.2817 Å2 / Biso min: 34.01 Å2
Refinement stepCycle: final / Resolution: 2.398→32.295 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5200 0 0 58 5258
Biso mean---57.79 -
Num. residues----666
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.398-2.4940.34781310.26712537266890
2.494-2.60740.32091460.25142688283494
2.6074-2.74480.32881440.23822754289897
2.7448-2.91670.28511440.23542748289297
2.9167-3.14170.28161500.22812727287796
3.1417-3.45760.24681430.19972785292898
3.4576-3.95710.21031420.17532779292197
3.9571-4.98260.16881540.15272822297699
4.9826-32.29770.24981460.16592817296398
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)
11.3073-0.54580.53021.314-0.2851.01-0.0268-0.0855-0.02380.2153-0.01070.0028-0.1126-0.03150.00010.4952-0.0328-0.01090.45390.03450.417619.811317.9589-13.5387
20.32720.0015-0.04940.6188-0.2030.7285-0.15790.0309-0.02810.2649-0.0566-0.2044-0.15160.4290.00030.4963-0.0732-0.10060.45980.06990.455729.224923.3716-13.3877
31.4461-1.47460.87172.626-0.92650.7879-0.02660.14040.12340.2054-0.04840.1604-0.1368-0.13290.00050.46240.00730.01870.45660.00590.51797.814135.7589-29.7255
40.31420.0419-0.33310.0226-0.15730.58170.10280.51610.2662-0.59270.0076-0.08810.06640.103500.66730.02150.01680.57750.08820.524821.42753.9813-51.8154
50.9655-0.3823-0.5310.8138-0.42780.71520.0634-0.1113-0.0330.0726-0.07530.08170.1503-0.0285-0.00030.44080.0039-0.02570.44480.03680.405115.6717-7.7262-32.6424
60.07320.1568-0.04590.4104-0.13410.0801-0.3769-0.32350.01740.0013-0.2180.84810.3306-0.0408-0.03080.51550.0163-0.03530.40140.02910.435610.683-6.744-48.6468
70.6460.3430.0480.8926-0.40691.4923-0.0659-0.07080.0769-0.661-0.08250.03890.16820.1081-0.05820.56370.04990.09020.42420.04680.335521.727-7.8717-46.5554
80.11820.0258-0.01930.07410.06890.02940.1133-0.15750.0399-0.4053-0.0558-0.4813-0.30820.66930.01340.41490.11180.03220.55680.0880.486929.5536-7.7569-36.1765
91.025-0.0859-0.72531.0055-0.97151.54450.0352-0.3691-0.4059-0.38-0.1815-0.02960.46380.064-0.00010.49950.00980.0130.40230.05390.513113.7052-17.7275-31.445
101.01830.0124-0.26410.4690.09320.85610.0364-0.0115-0.34030.1194-0.01010.040.0757-0.08570.00020.3792-0.03490.0140.55830.06980.6128-2.4939-23.2209-17.4698
110.2794-0.2519-0.11780.5731-0.18340.26590.06060.07780.34-0.0995-0.06780.72160.13770.057900.5074-0.0050.00310.52320.07750.7275-1.8196-6.7145-25.2236
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 83 through 219 )A83 - 219
2X-RAY DIFFRACTION2chain 'A' and (resid 220 through 305 )A220 - 305
3X-RAY DIFFRACTION3chain 'A' and (resid 306 through 430 )A306 - 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 264 )B203 - 264
8X-RAY DIFFRACTION8chain 'B' and (resid 265 through 296 )B265 - 296
9X-RAY DIFFRACTION9chain 'B' and (resid 297 through 357 )B297 - 357
10X-RAY DIFFRACTION10chain 'B' and (resid 358 through 408 )B358 - 408
11X-RAY DIFFRACTION11chain 'B' and (resid 409 through 430 )B409 - 430

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