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- PDB-5syp: Crystal Structure of ATPase delta1-79 Spa47 K165A -

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Basic information

Entry
Database: PDB / ID: 5syp
TitleCrystal Structure of ATPase delta1-79 Spa47 K165A
ComponentsProbable ATP synthase SpaL/MxiB
KeywordsHYDROLASE / 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 complex, catalytic core F(1) / 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 / 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: 2.15 Å
AuthorsMorales, Y. / Johnson, S.J. / Burgess, J.L. / Burgess, R.A. / Dickenson, N.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1K22AI099086-01A1 United States
CitationJournal: J. Biol. Chem. / Year: 2016
Title: Structural and Biochemical Characterization of Spa47 Provides Mechanistic Insight into Type III Secretion System ATPase Activation and Shigella Virulence Regulation.
Authors: Burgess, J.L. / Burgess, R.A. / Morales, Y. / Bouvang, J.M. / Johnson, S.J. / Dickenson, N.E.
History
DepositionAug 11, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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

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Assembly

Deposited unit
A: Probable ATP synthase SpaL/MxiB
B: Probable ATP synthase SpaL/MxiB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,3254
Polymers78,1332
Non-polymers1922
Water6,738374
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A: Probable ATP synthase SpaL/MxiB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1622
Polymers39,0661
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Probable ATP synthase SpaL/MxiB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1622
Polymers39,0661
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.401, 154.064, 54.938
Angle α, β, γ (deg.)90.000, 110.290, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Probable ATP synthase SpaL/MxiB / SPA47


Mass: 39066.355 Da / Num. of mol.: 2 / Fragment: UNP residues 80-430 / Mutation: K165A
Source method: isolated from a genetically manipulated source
Details: K165A / Source: (gene. exp.) Shigella flexneri (bacteria) / Strain: 2457T / 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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 374 / 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: 2.27 Å3/Da / Density % sol: 45.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.5
Details: Tris, Ammonium Acetate, Lithium Sulfate, PEG 4000, MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.97946 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 1, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 37584 / % possible obs: 100 % / Redundancy: 5 % / Biso Wilson estimate: 32.06 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.131 / Net I/av σ(I): 15.059 / Net I/σ(I): 6.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.15-2.234.31.1030.4811100
2.23-2.324.70.9810.591100
2.32-2.424.90.7670.7131100
2.42-2.5550.5910.8121100
2.55-2.7150.4180.9031100
2.71-2.925.10.2740.9581100
2.92-3.215.20.1580.9851100
3.21-3.685.30.090.9951100
3.68-4.635.40.0510.9981100
4.63-505.30.0430.998199.9

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5SWJ

5swj


Resolution: 2.15→42.831 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.24
RfactorNum. reflection% reflection
Rfree0.2324 1874 4.99 %
Rwork0.1941 --
obs0.196 37547 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 207.17 Å2 / Biso mean: 42.7445 Å2 / Biso min: 15.97 Å2
Refinement stepCycle: final / Resolution: 2.15→42.831 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5308 0 10 374 5692
Biso mean--72.98 44.08 -
Num. residues----681
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035417
X-RAY DIFFRACTIONf_angle_d0.7147319
X-RAY DIFFRACTIONf_chiral_restr0.025837
X-RAY DIFFRACTIONf_plane_restr0.004942
X-RAY DIFFRACTIONf_dihedral_angle_d12.6422010
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1494-2.20750.3121490.2632763291299
2.2075-2.27240.2721360.253526952831100
2.2724-2.34580.30671500.246127512901100
2.3458-2.42960.27291430.235427152858100
2.4296-2.52690.24531350.228727452880100
2.5269-2.64190.2951420.230327682910100
2.6419-2.78110.29851500.225427412891100
2.7811-2.95530.28411430.221727202863100
2.9553-3.18350.26731440.214427532897100
3.1835-3.50370.23751420.200127412883100
3.5037-4.01040.21231510.170127462897100
4.0104-5.05130.18251450.14527492894100
5.0513-42.8390.16581440.160127862930100
Refinement TLS params.Method: refined / Origin x: 60.1205 Å / Origin y: 8.5555 Å / Origin z: -27.382 Å
111213212223313233
T0.139 Å2-0.0147 Å2-0.0011 Å2-0.236 Å20.0366 Å2--0.1905 Å2
L0.3917 °2-0.0179 °20.0217 °2-0.8908 °2-0.1572 °2--0.5662 °2
S-0.0395 Å °-0.0174 Å °-0.0187 Å °-0.0296 Å °0.0082 Å °-0.052 Å °0.007 Å °-0.0468 Å °0.0177 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA82 - 430
2X-RAY DIFFRACTION1allB82 - 430
3X-RAY DIFFRACTION1allC1 - 2
4X-RAY DIFFRACTION1allS1 - 375

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