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- PDB-6dcs: Stage III sporulation protein AF (SpoIIIAF) -

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Basic information

Entry
Database: PDB / ID: 6dcs
TitleStage III sporulation protein AF (SpoIIIAF)
ComponentsStage III sporulation protein AF
KeywordsPROTEIN TRANSPORT / Secretion system / Sporulation / Ring Building Motif (RBM)
Function / homologySporulation stage III, protein AF / Stage III sporulation protein AF (Spore_III_AF) / sporulation resulting in formation of a cellular spore / plasma membrane / Stage III sporulation protein AF
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsStrynadka, N.C.J. / Zeytuni, N. / Camp, A.H. / Flanagan, K.A.
CitationJournal: J. Struct. Biol. / Year: 2018
Title: Structural and biochemical characterization of SpoIIIAF, a component of a sporulation-essential channel in Bacillus subtilis.
Authors: Zeytuni, N. / Flanagan, K.A. / Worrall, L.J. / Massoni, S.C. / Camp, A.H. / Strynadka, N.C.J.
History
DepositionMay 8, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2018Group: Data collection / Database references / Source and taxonomy
Category: citation / entity_src_gen
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Stage III sporulation protein AF
B: Stage III sporulation protein AF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5345
Polymers28,2462
Non-polymers2883
Water00
1
A: Stage III sporulation protein AF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3153
Polymers14,1231
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Stage III sporulation protein AF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2192
Polymers14,1231
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)119.365, 119.365, 40.861
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Stage III sporulation protein AF


Mass: 14122.787 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: spoIIIAF, BSU24380 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P49783
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4

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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: 2.78 Å3/Da / Density % sol: 55.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 2M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.286 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.286 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 8421 / % possible obs: 98 % / Redundancy: 6.7 % / Biso Wilson estimate: 63.74 Å2 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.034 / Rrim(I) all: 0.091 / Χ2: 2.445 / Net I/σ(I): 11.6 / Num. measured all: 56622
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.753.70.3043320.9750.1570.3451.44780
2.75-2.84.40.343670.9360.1590.3781.11189.3
2.8-2.855.20.273990.9870.1230.2981.03393.9
2.85-2.9160.2234100.9890.0960.2431.08698.6
2.91-2.976.50.2424090.9910.1010.2631.12199.8
2.97-3.046.80.2284160.9840.0930.2471.346100
3.04-3.127.30.1944240.980.0760.2091.49100
3.12-3.28.10.1934170.9870.0730.2071.477100
3.2-3.38.20.1544200.990.0580.1651.785100
3.3-3.47.80.1364370.9970.0530.1462.029100
3.4-3.526.40.1464100.9840.0620.1592.79899.8
3.52-3.666.90.1184230.9910.050.1292.85999.5
3.66-3.836.70.0994280.9980.0420.1073.13399.8
3.83-4.036.60.0974280.9930.0410.1053.361100
4.03-4.297.60.0814230.9950.0320.0873.145100
4.29-4.627.40.0754400.9970.030.0813.396100
4.62-5.086.70.0744400.9960.0310.083.67699.8
5.08-5.817.70.0764450.9960.030.0823.327100
5.81-7.327.10.0674450.9970.0260.0723.21399.6
7.32-506.40.0575080.9970.0240.0623.85399.8

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→38.659 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 37.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2994 427 5.11 %
Rwork0.24 7932 -
obs0.2431 8359 97.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 117.13 Å2 / Biso mean: 66.3687 Å2 / Biso min: 38.83 Å2
Refinement stepCycle: final / Resolution: 2.7→38.659 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1834 0 15 0 1849
Biso mean--82 --
Num. residues----233
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111870
X-RAY DIFFRACTIONf_angle_d1.2382513
X-RAY DIFFRACTIONf_chiral_restr0.064280
X-RAY DIFFRACTIONf_plane_restr0.006321
X-RAY DIFFRACTIONf_dihedral_angle_d8.9631148
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7004-3.0910.37861160.28122467258393
3.091-3.89380.29311600.260926382798100
3.8938-38.66260.291510.222928272978100

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