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- PDB-6n72: Crystal Structure of ATPase delta1-79 Spa47 E267R -

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Basic information

Entry
Database: PDB / ID: 6n72
TitleCrystal Structure of ATPase delta1-79 Spa47 E267R
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 / MOLECULAR REPLACEMENT / Resolution: 2.735 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)78,3052
Polymers78,3052
Non-polymers00
Water1,15364
1
A: ATP synthase SpaL/MxiB


Theoretical massNumber of molelcules
Total (without water)39,1531
Polymers39,1531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ATP synthase SpaL/MxiB


Theoretical massNumber of molelcules
Total (without water)39,1531
Polymers39,1531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.965, 153.823, 54.793
Angle α, β, γ (deg.)90.000, 109.900, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ATP synthase SpaL/MxiB


Mass: 39152.539 Da / Num. of mol.: 2 / Mutation: delta 1-79, E267R
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.: 64 / 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: 2.22 Å3/Da / Density % sol: 44.71 % / Mosaicity: 1.262 °
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: 2.75→50 Å / Num. obs: 17714 / % possible obs: 98.6 % / Redundancy: 6.8 % / Biso Wilson estimate: 40.23 Å2 / Rmerge(I) obs: 0.248 / Rpim(I) all: 0.101 / Rrim(I) all: 0.268 / Χ2: 0.744 / Net I/σ(I): 2.6 / Num. measured all: 121252
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.75-2.856.91.22517080.6480.5011.3260.48799.2
2.85-2.966.90.93418070.7590.3821.0110.50599
2.96-3.16.70.71817410.8380.2980.7790.53997.8
3.1-3.266.40.51117340.8880.2160.5570.61396.5
3.26-3.467.20.38217970.9340.1530.4120.68199.7
3.46-3.737.10.27317780.9660.1090.2940.76899.4
3.73-4.1170.20717950.9780.0840.2240.83499.4
4.11-4.76.40.14417530.9840.0610.1570.92197.7
4.7-5.927.20.14117990.9880.0570.1520.79499.6
5.92-506.80.10918020.9930.0440.1181.27998.1

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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: 2.735→41.339 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2461 879 4.97 %
Rwork0.1929 16807 -
obs0.1956 17686 98.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 143.92 Å2 / Biso mean: 45.3917 Å2 / Biso min: 12.53 Å2
Refinement stepCycle: final / Resolution: 2.735→41.339 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5248 0 0 64 5312
Biso mean---31.38 -
Num. residues----671
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7351-2.90650.3241420.27252707284995
2.9065-3.13080.29941490.25072770291998
3.1308-3.44570.27431410.22132814295599
3.4457-3.9440.25161520.18872847299999
3.944-4.96770.21991480.15512820296898
4.9677-41.34390.20121470.16622849299699
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)
12.6552-0.5068-0.73991.0087-0.20191.53480.2114-0.3289-0.26760.5088-0.168-0.28450.07920.1962-0.01630.30920.0083-0.05780.30890.11750.268425.10028.4102-6.2315
21.6669-0.39650.21921.0638-0.17670.02960.0867-0.1658-0.12040.1058-0.0492-0.084-0.09710.0251-0.03690.303-0.03110.0230.32460.02970.207219.582123.41-23.1447
32.5898-0.1603-0.37391.2526-1.47121.8726-0.0144-0.3890.26820.30090.04180.3641-0.4132-0.16070.00370.3185-0.04740.04650.2893-0.00150.304815.959318.5637-7.2094
41.9356-0.1067-0.25122.02950.24342.1125-0.0083-0.12450.22550.3047-0.0527-0.0891-0.19290.15640.00720.2545-0.0367-0.03680.26680.03910.292729.089623.3188-13.7345
50.54590.5338-0.70910.83150.04762.69160.2461-0.06721.026-0.03960.01750.5556-1.4175-0.0532-0.02620.6757-0.0627-0.03020.57540.10170.849323.150140.4249-16.6446
61.9263-1.27220.42022.5419-0.11450.0879-0.06650.08590.19950.1439-0.04660.034-0.1057-0.04950.10060.27530.01060.01980.27260.02450.28695.497935.1387-31.3209
73.39360.58880.40081.37570.04191.68420.06640.13570.1935-0.31290.16820.1799-0.3447-0.1984-0.09170.36480.03490.05260.32650.09440.213821.49613.9218-51.8085
81.26020.70311.09110.80080.35711.08510.1432-0.0534-0.08710.0984-0.1513-0.1368-0.15820.2133-0.08960.26930.0192-0.05640.2350.04880.302124.7663-2.5525-30.3369
91.58580.1357-0.73311.8582-1.31891.1856-0.10330.269-0.0787-0.2904-0.08970.19590.2543-0.15560.04730.3117-0.0163-0.04490.3118-0.03310.277810.363-9.1696-40.4507
101.2168-0.3505-0.3012.0998-0.15842.3039-0.06720.2977-0.3-0.6322-0.02210.1720.12220.23710.06080.28630.01880.01020.2903-0.01540.207321.8558-7.957-46.3737
112.38540.3627-0.20022.17160.00113.0872-0.16020.0623-0.69610.1168-0.0246-0.15880.50210.43850.12230.31130.10520.02620.29820.05430.400723.136-15.3265-35.9763
122.35941.2759-0.73731.4278-0.76990.7102-0.0283-0.0828-0.32590.0456-0.0398-0.10780.1047-0.08150.03640.230.0127-0.02660.28510.03420.30942.3861-20.8809-21.8144
132.97160.30840.85133.41260.33462.8614-0.1469-0.1965-0.19960.09910.02740.37440.0964-0.1256-0.03470.2584-0.00750.02570.28150.05240.321-1.7315-6.9741-25.1234
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 83 through 118 )A83 - 118
2X-RAY DIFFRACTION2chain 'A' and (resid 119 through 175 )A119 - 175
3X-RAY DIFFRACTION3chain 'A' and (resid 176 through 219 )A176 - 219
4X-RAY DIFFRACTION4chain 'A' and (resid 220 through 305 )A220 - 305
5X-RAY DIFFRACTION5chain 'A' and (resid 306 through 322 )A306 - 322
6X-RAY DIFFRACTION6chain 'A' and (resid 323 through 430 )A323 - 430
7X-RAY DIFFRACTION7chain 'B' and (resid 83 through 118 )B83 - 118
8X-RAY DIFFRACTION8chain 'B' and (resid 119 through 140 )B119 - 140
9X-RAY DIFFRACTION9chain 'B' and (resid 141 through 202 )B141 - 202
10X-RAY DIFFRACTION10chain 'B' and (resid 203 through 264 )B203 - 264
11X-RAY DIFFRACTION11chain 'B' and (resid 265 through 322 )B265 - 322
12X-RAY DIFFRACTION12chain 'B' and (resid 323 through 408 )B323 - 408
13X-RAY DIFFRACTION13chain 'B' and (resid 409 through 430 )B409 - 430

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