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- PDB-6n6z: Crystal Structure of ATPase delta 1-79 Spa47 R189E -

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Basic information

Entry
Database: PDB / ID: 6n6z
TitleCrystal Structure of ATPase delta 1-79 Spa47 R189E
ComponentsProbable ATP 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: 2.642 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: Probable ATP synthase SpaL/MxiB
B: Probable ATP synthase SpaL/MxiB


Theoretical massNumber of molelcules
Total (without water)78,1932
Polymers78,1932
Non-polymers00
Water52229
1
A: Probable ATP synthase SpaL/MxiB


Theoretical massNumber of molelcules
Total (without water)39,0961
Polymers39,0961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable ATP synthase SpaL/MxiB


Theoretical massNumber of molelcules
Total (without water)39,0961
Polymers39,0961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.824, 153.726, 54.746
Angle α, β, γ (deg.)90.000, 109.670, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Probable ATP synthase SpaL/MxiB


Mass: 39096.379 Da / Num. of mol.: 2 / Mutation: delta 1-79, R189E
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.: 29 / 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: 44.61 % / Mosaicity: 1.189 °
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: 0.954 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: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 19703 / % possible obs: 98.5 % / Redundancy: 7.7 % / Biso Wilson estimate: 57.51 Å2 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.064 / Rrim(I) all: 0.182 / Χ2: 0.866 / Net I/σ(I): 3.7 / Num. measured all: 150751
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.65-2.745.41.27119330.5460.5811.4040.51294.9
2.74-2.856.81.1219320.7220.4521.2110.50399.2
2.85-2.987.70.86319810.8350.3270.9240.50499.4
2.98-3.1480.60419850.9170.2220.6440.55199.4
3.14-3.348.10.41819840.9510.1530.4460.60899.2
3.34-3.67.60.27919300.9780.1070.30.74197.1
3.6-3.968.40.18519940.9890.0670.1970.90999.6
3.96-4.538.30.12119920.9930.0440.1291.02799.8
4.53-5.717.80.09819660.9940.0370.1051.09198.3
5.71-508.20.09520060.9940.0360.1011.94998.5

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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: 2.642→36.342 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2726 980 4.98 %
Rwork0.2146 18684 -
obs0.2176 19664 98.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 254.43 Å2 / Biso mean: 72.2197 Å2 / Biso min: 26.18 Å2
Refinement stepCycle: final / Resolution: 2.642→36.342 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5218 0 0 29 5247
Biso mean---48.4 -
Num. residues----668
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6417-2.7810.36221290.3152583271295
2.781-2.95510.30461440.290126862830100
2.9551-3.18320.32691440.27082694283899
3.1832-3.50330.28821370.24562654279199
3.5033-4.00960.26011440.20752676282098
4.0096-5.04960.26411430.18122697284099
5.0496-36.34530.24211390.18292694283398
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)
12.8737-0.8583-0.34261.988-0.43262.9128-0.0096-0.4247-0.2950.9727-0.10040.04680.09780.10710.21740.699-0.0258-0.06770.51070.11810.444923.39918.4888-5.8584
20.7511-0.7592-0.56022.6361-0.68381.67640.0893-0.0882-0.04040.0065-0.2504-0.658-0.44610.62880.4140.4831-0.08250.00230.68560.1290.71229.628316.6263-23.4663
31.5552-1.60931.45473.0264-2.55171.912-0.1783-0.1550.05540.8476-0.00190.0673-0.6216-0.07730.09930.7617-0.05980.01430.49460.01230.47813.991923.192-15.4556
45.18280.97610.91994.6013-1.07832.4134-0.4981-0.77430.5170.9254-0.13921.0185-0.55470.10390.22590.5737-0.0026-0.10220.51530.04980.495918.028316.789-6.5888
52.5260.46870.26223.36590.0752.4596-0.0771-0.08130.211.0589-0.238-0.3234-0.8250.59720.20640.869-0.205-0.2260.52430.12190.588227.838922.2769-10.7304
61.835-0.23650.85911.17390.03830.3202-0.2487-0.26170.61430.1819-0.0587-0.4063-0.62230.65650.28240.6749-0.2349-0.17120.69250.11780.845531.182124.5916-17.9212
73.9266-1.03211.09063.9856-1.44712.9311-0.2761-0.23390.62391.061-0.0201-0.329-0.97690.20220.12790.8524-0.0449-0.07450.42060.01150.594116.779135.0332-23.3804
84.0995-3.0324-1.25669.53972.05122.26270.2249-0.24331.2175-0.20210.2763-0.9835-0.30740.1622-0.05020.3575-0.02850.00750.46130.10460.45526.809438.5473-36.0484
92.8054-1.22260.85415.5519-1.05620.11910.0425-0.0810.0991-0.050.03350.7562-0.0556-0.1784-0.12860.40290.04910.04850.5409-0.00090.6829-0.778434.5264-33.1511
103.8188-0.1416-0.37723.1369-0.34362.8515-0.08120.54930.3199-0.63790.28660.2401-0.06430.22140.18530.63810.03970.06530.51340.12150.501821.03623.896-51.9935
111.01360.03880.8192.6496-0.00362.49590.6829-0.2050.71520.0294-0.4448-0.5838-0.01910.68370.21830.43280.09160.00870.52890.1150.494524.5384-2.5286-30.4619
122.66180.794-0.83043.096-0.91322.4497-0.0970.2396-0.1722-0.9247-0.0848-0.06590.63560.12750.0750.57890.09830.05630.35960.00780.363515.9223-8.5615-43.6059
132.8894-0.38910.15683.64560.43824.65540.13910.1142-0.7043-0.1798-0.2683-0.5481.22350.18790.11770.71540.10050.08650.63450.11650.617522.7134-15.1894-36.5717
143.34431.519-0.87733.4457-1.56042.1284-0.0077-0.1767-0.5057-0.1949-0.09190.21960.3132-0.1041-0.10820.35010.0268-0.03440.41910.03380.48892.6948-20.7772-21.9915
152.8051-0.24480.05585.771-1.40924.37970.1008-0.1596-0.4763-0.16560.1020.8643-0.1004-0.3633-0.18670.37440.00520.00910.54930.08230.8239-1.7576-6.8195-25.0984
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 140 )A115 - 140
3X-RAY DIFFRACTION3chain 'A' and (resid 141 through 202 )A141 - 202
4X-RAY DIFFRACTION4chain 'A' and (resid 203 through 219 )A203 - 219
5X-RAY DIFFRACTION5chain 'A' and (resid 220 through 263 )A220 - 263
6X-RAY DIFFRACTION6chain 'A' and (resid 264 through 305 )A264 - 305
7X-RAY DIFFRACTION7chain 'A' and (resid 306 through 357 )A306 - 357
8X-RAY DIFFRACTION8chain 'A' and (resid 358 through 382 )A358 - 382
9X-RAY DIFFRACTION9chain 'A' and (resid 383 through 430 )A383 - 430
10X-RAY DIFFRACTION10chain 'B' and (resid 83 through 118 )B83 - 118
11X-RAY DIFFRACTION11chain 'B' and (resid 119 through 140 )B119 - 140
12X-RAY DIFFRACTION12chain 'B' and (resid 141 through 264 )B141 - 264
13X-RAY DIFFRACTION13chain 'B' and (resid 265 through 320 )B265 - 320
14X-RAY DIFFRACTION14chain 'B' and (resid 321 through 408 )B321 - 408
15X-RAY DIFFRACTION15chain 'B' and (resid 409 through 430 )B409 - 430

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