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- PDB-6n76: Crystal Structure of ATPase delta1-79 Spa47 E287R -

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Basic information

Entry
Database: PDB / ID: 6n76
TitleCrystal Structure of ATPase delta1-79 Spa47 E287R
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: 2.892 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
Water0
1
A: ATP synthase SpaL/MxiB


Theoretical massNumber of molelcules
Total (without water)39,1531
Polymers39,1531
Non-polymers00
Water0
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
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.513, 154.748, 54.965
Angle α, β, γ (deg.)90.000, 109.300, 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, E287R
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

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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: 2.23 Å3/Da / Density % sol: 44.85 % / Mosaicity: 1.349 °
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: 2.9→50 Å / Num. obs: 14991 / % possible obs: 98.5 % / Redundancy: 4.6 % / Biso Wilson estimate: 52.78 Å2 / Rmerge(I) obs: 0.212 / Rpim(I) all: 0.108 / Rrim(I) all: 0.239 / Χ2: 0.785 / Net I/σ(I): 3.3 / Num. measured all: 69099
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.9-34.81.30814570.5170.6581.470.51399.7
3-3.124.70.84815150.6990.4270.9530.53599.3
3.12-3.274.70.64515140.8020.3260.7250.56199
3.27-3.444.60.43815050.8820.2230.4930.59198.7
3.44-3.654.70.33114980.9360.1680.3720.69797.8
3.65-3.944.20.23614680.9440.1270.270.88496.6
3.94-4.334.50.17514830.9720.0910.1980.88898.2
4.33-4.964.80.12515100.9840.0620.140.95699.5
4.96-6.244.70.13715290.9840.0690.1540.83699.4
6.24-504.50.08115120.9950.040.091.44297.2

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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: 2.892→34.895 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2437 741 4.95 %
Rwork0.1879 14225 -
obs0.1908 14966 97.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 188.82 Å2 / Biso mean: 61.057 Å2 / Biso min: 20.82 Å2
Refinement stepCycle: final / Resolution: 2.892→34.895 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5176 0 0 0 5176
Num. residues----661
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 (%)
2.8918-3.11490.31011470.24842762290996
3.1149-3.42810.28231450.22052876302199
3.4281-3.92360.26861460.19392818296497
3.9236-4.94110.20591520.15932869302199
4.9411-34.89760.22621510.17522900305199
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)
12.4893-0.68370.95882.7322-1.33872.9580.015-0.3401-0.15950.57730.0004-0.0885-0.3560.1077-0.01480.4137-0.03560.01480.29920.05810.252219.539318.0932-13.7436
22.1925-0.3953-0.66982.18690.49242.2186-0.4107-0.01340.07160.46860.0727-0.4252-0.66610.93520.1160.518-0.1761-0.20910.42080.11610.416828.558823.0695-13.8393
34.0894-2.29360.78244.7546-0.66151.3913-0.10150.01160.53960.3679-0.1724-0.168-0.0555-0.14130.26910.33790.00960.03030.34150.06320.42848.789438.7315-29.8198
45.2408-0.7108-0.31286.9963-0.65724.74110.06540.064-0.51170.1347-0.03381.0214-0.1097-0.7123-0.24690.17330.00710.06330.35050.03590.65612.129124.146-31.0876
51.32180.263-0.48371.5311-0.44012.63370.07960.12250.2178-0.2650.0564-0.1831-0.11010.247-0.10670.4090.070.0290.40340.02740.25521.96981.5611-43.9594
62.30730.1712-0.69532.5696-0.96822.9299-0.03030.4425-0.1222-0.925-0.0617-0.00880.40990.03960.0390.49890.07230.00140.35310.02080.217615.521-8.401-43.7386
72.93560.6444-1.57760.94510.26173.1384-0.3948-0.2805-0.55240.27270.0939-0.17610.68380.50310.23960.35480.13230.02980.38290.11990.437622.9363-14.1127-35.5085
81.83511.3162-1.00173.7016-1.39081.27660.1117-0.0226-0.21980.0089-0.14530.5120.0094-0.08310.02810.2154-0.0210.0110.38770.00970.48910.2357-17.9003-22.0539
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 408 )A306 - 408
4X-RAY DIFFRACTION4chain 'A' and (resid 409 through 430 )A409 - 430
5X-RAY DIFFRACTION5chain 'B' and (resid 83 through 140 )B83 - 140
6X-RAY DIFFRACTION6chain 'B' and (resid 141 through 263 )B141 - 263
7X-RAY DIFFRACTION7chain 'B' and (resid 264 through 330 )B264 - 330
8X-RAY DIFFRACTION8chain 'B' and (resid 331 through 430 )B331 - 430

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