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- PDB-5of2: The structural versatility of TasA in B. subtilis biofilm formation -

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Basic information

Entry
Database: PDB / ID: 5of2
TitleThe structural versatility of TasA in B. subtilis biofilm formation
ComponentsSpore coat-associated protein N
KeywordsPROTEIN FIBRIL / TasA / biofilm matrix / amyloid fiber / xray structure
Function / homologyPeptidase M73, camelysin / Camelysin metallo-endopeptidase / Signal peptide, camelysin / sporulation resulting in formation of a cellular spore / extracellular region / identical protein binding / Major biofilm matrix component
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsRoske, Y. / Diehl, A. / Ball, L. / Chowdhury, A. / Hiller, M. / Moliere, N. / Kramer, R. / Nagaraj, M. / Stoeppler, D. / Worth, C.L. ...Roske, Y. / Diehl, A. / Ball, L. / Chowdhury, A. / Hiller, M. / Moliere, N. / Kramer, R. / Nagaraj, M. / Stoeppler, D. / Worth, C.L. / Schlegel, B. / Leidert, M. / Cremer, N. / Eisenmenger, F. / Lopez, D. / Schmieder, P. / Heinemann, U. / Turgay, K. / Akbey, U. / Oschkinat, H.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Structural changes of TasA in biofilm formation ofBacillus subtilis.
Authors: Diehl, A. / Roske, Y. / Ball, L. / Chowdhury, A. / Hiller, M. / Moliere, N. / Kramer, R. / Stoppler, D. / Worth, C.L. / Schlegel, B. / Leidert, M. / Cremer, N. / Erdmann, N. / Lopez, D. / ...Authors: Diehl, A. / Roske, Y. / Ball, L. / Chowdhury, A. / Hiller, M. / Moliere, N. / Kramer, R. / Stoppler, D. / Worth, C.L. / Schlegel, B. / Leidert, M. / Cremer, N. / Erdmann, N. / Lopez, D. / Stephanowitz, H. / Krause, E. / van Rossum, B.J. / Schmieder, P. / Heinemann, U. / Turgay, K. / Akbey, U. / Oschkinat, H.
History
DepositionJul 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.2Apr 11, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _citation.journal_volume ..._chem_comp.name / _citation.journal_volume / _citation.page_first / _citation.page_last / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.3Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spore coat-associated protein N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2555
Polymers22,9731
Non-polymers2824
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area680 Å2
ΔGint4 kcal/mol
Surface area10120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.658, 43.039, 51.693
Angle α, β, γ (deg.)90.00, 90.17, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Spore coat-associated protein N / TasA / structure / biofilm / matrix protein


Mass: 22972.691 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Gene: tasA, cotN, yqhF, BSU24620 / Plasmid: pCA528 / Production host: Escherichia coli (E. coli) / Strain (production host): T7 Express / References: UniProt: P54507
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.02 Å3/Da / Density % sol: 39.02 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.8
Details: 34% PEG 2000 MME, 0.1M ammonium sulfate, 0.1M sodium acetate pH 4.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.86→41.66 Å / Num. obs: 15615 / % possible obs: 99.63 % / Redundancy: 4.5 % / Biso Wilson estimate: 21.48 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.083 / Net I/σ(I): 13.83
Reflection shellResolution: 1.86→1.92 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.7454 / Mean I/σ(I) obs: 1.85 / Num. unique obs: 1542 / CC1/2: 0.804 / % possible all: 97.84

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OF1

5of1


Resolution: 1.86→41.658 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 24.42
RfactorNum. reflection% reflection
Rfree0.2118 781 5 %
Rwork0.1726 --
obs0.1747 15608 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.86→41.658 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1458 0 17 142 1617
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071509
X-RAY DIFFRACTIONf_angle_d0.9882032
X-RAY DIFFRACTIONf_dihedral_angle_d15.344560
X-RAY DIFFRACTIONf_chiral_restr0.043229
X-RAY DIFFRACTIONf_plane_restr0.005265
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8567-1.9730.2981280.2672430X-RAY DIFFRACTION98
1.973-2.12530.26041290.19732447X-RAY DIFFRACTION100
2.1253-2.33920.21461300.18192469X-RAY DIFFRACTION100
2.3392-2.67760.22871290.16842461X-RAY DIFFRACTION100
2.6776-3.37330.20031310.16892481X-RAY DIFFRACTION100
3.3733-41.66830.18311340.15192539X-RAY DIFFRACTION100
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)
10.6260.0005-0.52331.1904-0.09012.299-0.0397-0.0799-0.00420.17920.0198-0.0820.0860.35250.0210.1186-0.0011-0.0150.159-0.00320.1458-11.2362-2.2156-19.6763
20.2199-0.04960.02310.17360.00823.90140.0648-0.0150.00180.01960.0613-0.0842-0.24550.2334-0.19770.1459-0.01740.01540.1361-0.00160.1663-10.75383.6979-22.1765
30.05640.25430.24731.649-0.1874.3184-0.10820.3450.3595-0.09820.33110.42750.2688-0.2357-0.16960.3359-0.1343-0.08190.26910.09730.3097-20.4743-8.4683-46.8196
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 39 through 201 )
2X-RAY DIFFRACTION2chain 'A' and (resid 214 through 238 )
3X-RAY DIFFRACTION3chain 'A' and (resid 202 through 213 )

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