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- PDB-6n75: Crystal Structure of ATPase delta1-79 Spa47 E287A -

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Basic information

Entry
Database: PDB / ID: 6n75
TitleCrystal Structure of ATPase delta1-79 Spa47 E287A
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 ...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: 2.991 Å
AuthorsMorales, Y. / Olsen, K.J. / 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)78,1332
Polymers78,1332
Non-polymers00
Water1267
1
A: ATP synthase SpaL/MxiB


Theoretical massNumber of molelcules
Total (without water)39,0661
Polymers39,0661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ATP synthase SpaL/MxiB


Theoretical massNumber of molelcules
Total (without water)39,0661
Polymers39,0661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.166, 153.241, 54.422
Angle α, β, γ (deg.)90.000, 109.410, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ATP synthase SpaL/MxiB


Mass: 39066.422 Da / Num. of mol.: 2 / Mutation: delta 1-79, E287A
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


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.17 Å3/Da / Density % sol: 43.39 % / Mosaicity: 1.339 °
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: 1.072 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: 1.072 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 13199 / % possible obs: 98.9 % / Redundancy: 5.3 % / Biso Wilson estimate: 53.84 Å2 / Rmerge(I) obs: 0.217 / Rpim(I) all: 0.104 / Rrim(I) all: 0.241 / Χ2: 1.513 / Net I/σ(I): 5 / Num. measured all: 69453
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3-3.114.40.9113030.6620.4781.0330.56498.9
3.11-3.234.90.75713200.7490.3750.8480.56899.1
3.23-3.385.10.5913290.8680.2860.6580.68699
3.38-3.564.70.4912810.8260.250.5531.396.6
3.56-3.785.50.41813070.9250.1990.4641.97899.4
3.78-4.075.60.28613470.9590.1340.3171.88699.9
4.07-4.485.70.16513220.980.0760.1821.60299.5
4.48-5.135.40.13813080.9810.0650.1531.89698.5
5.13-6.465.80.13813350.9850.0630.1521.51999.1
6.46-505.60.07413470.9950.0350.0822.60898.8

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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: 2.991→42.644 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.271 653 4.97 %
Rwork0.2195 12481 -
obs0.2222 13134 97.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 179.05 Å2 / Biso mean: 63.9048 Å2 / Biso min: 10.33 Å2
Refinement stepCycle: final / Resolution: 2.991→42.644 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5098 0 0 7 5105
Biso mean---36.71 -
Num. residues----653
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 (%)
2.9913-3.22220.34521230.27192368249193
3.2222-3.54630.2991390.25522507264698
3.5463-4.05910.34611200.25142516263698
4.0591-5.11270.23441360.18552533266999
5.1127-42.64790.2271350.19312557269299
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)
16.73980.1653-0.62563.2233-0.46643.4922-0.0711-0.7062-0.69590.5457-0.4663-0.55030.18830.47960.44350.44950.0031-0.05330.32610.12130.347241.28898.1101-56.9518
22.2824-0.21521.77192.5718-1.95012.5583-0.1691-0.2388-0.11980.3304-0.0778-0.3099-0.33510.36930.1930.3669-0.0342-0.04170.34960.02860.387138.699321.5808-73.4806
32.31570.64620.39783.6746-0.95582.7016-0.2858-0.01740.38670.7067-0.0124-0.3305-0.73620.21290.16390.5031-0.1015-0.23180.33990.10450.525941.435222.7903-63.74
43.858-2.73990.82555.4002-1.42760.94930.08080.17060.38050.1298-0.1810.0267-0.096-0.080.04460.2368-0.0281-0.01570.36590.06550.494522.564934.6582-83.6693
50.41980.391-1.03662.3266-0.71843.63160.22720.15020.211-0.4077-0.1653-0.3553-0.16270.4874-0.08440.39210.11110.02080.51260.13120.424240.24650.9166-94.6145
61.90510.2586-1.60872.4946-2.40612.955-0.33380.4435-0.3117-0.765-0.0080.13230.7269-0.1660.33830.5140.0263-0.04930.4255-0.04880.403827.9639-9.7909-91.5903
72.85060.67860.08253.28480.20214.6775-0.17960.07-0.2579-0.7284-0.0897-0.40380.63120.29020.18190.48140.10970.13820.3530.1170.37740.1526-9.9114-93.8781
82.43391.408-1.34593.1144-1.53412.239-0.0733-0.0455-0.3127-0.2394-0.10480.21220.35360.0770.10370.2738-0.0004-0.02980.3489-0.01960.548320.7452-21.3163-72.8094
95.01840.08681.87956.73751.72626.7138-0.401-0.15110.23650.3913-0.49181.3013-0.1587-0.79730.45290.2952-0.0106-0.07210.39950.14160.573516.2506-7.208-76.0113
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 83 through 114 )A83 - 114
2X-RAY DIFFRACTION2chain 'A' and (resid 115 through 175 )A115 - 175
3X-RAY DIFFRACTION3chain 'A' and (resid 176 through 330 )A176 - 330
4X-RAY DIFFRACTION4chain 'A' and (resid 331 through 430 )A331 - 430
5X-RAY DIFFRACTION5chain 'B' and (resid 83 through 140 )B83 - 140
6X-RAY DIFFRACTION6chain 'B' and (resid 141 through 202 )B141 - 202
7X-RAY DIFFRACTION7chain 'B' and (resid 203 through 320 )B203 - 320
8X-RAY DIFFRACTION8chain 'B' and (resid 321 through 408 )B321 - 408
9X-RAY DIFFRACTION9chain 'B' and (resid 409 through 430 )B409 - 430

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