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- PDB-5of1: The structural versatility of TasA in B. subtilis biofilm formation -

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Basic information

Entry
Database: PDB / ID: 5of1
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 / 2-HYDROXYBENZOIC ACID / Major biofilm matrix component
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.56 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 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_modification_feature
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
B: Spore coat-associated protein N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7837
Polymers46,3212
Non-polymers4625
Water5,963331
1
A: Spore coat-associated protein N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4855
Polymers23,1601
Non-polymers3244
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Spore coat-associated protein N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2982
Polymers23,1601
Non-polymers1381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.728, 43.149, 51.744
Angle α, β, γ (deg.)89.92, 91.86, 90.01
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 23160.271 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: tasA, cotN, yqhF, BSU24620 / Plasmid: pCA528 / Production host: Escherichia coli (E. coli) / Strain (production host): T7 Express / References: UniProt: P54507
#2: Chemical ChemComp-SAL / 2-HYDROXYBENZOIC ACID / SALICYLIC ACID


Mass: 138.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.96 Å3/Da / Density % sol: 37.31 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.8
Details: 34% PEG2000 MME, 0.2M lithium salicylate, 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: 0.9797 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.524
11-H, K, -L20.476
ReflectionResolution: 1.56→40.71 Å / Num. obs: 47368 / % possible obs: 96.33 % / Redundancy: 4.1 % / Biso Wilson estimate: 24.363 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.0777 / Net I/σ(I): 13.33
Reflection shellResolution: 1.56→1.614 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.4156 / Mean I/σ(I) obs: 2.73 / Num. unique obs: 4658 / CC1/2: 0.921 / % possible all: 93.31

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
XDSdata reduction
XDSdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.56→40.71 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.969 / SU B: 0.964 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.016 / ESU R Free: 0.016 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17523 1080 2.2 %RANDOM
Rwork0.15222 ---
obs0.15273 47368 96.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.363 Å2
Baniso -1Baniso -2Baniso -3
1-17.74 Å23.42 Å2-1.01 Å2
2---0.77 Å21.91 Å2
3----16.97 Å2
Refinement stepCycle: 1 / Resolution: 1.56→40.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3007 0 32 331 3370
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.023125
X-RAY DIFFRACTIONr_bond_other_d0.0020.022985
X-RAY DIFFRACTIONr_angle_refined_deg1.8421.9854216
X-RAY DIFFRACTIONr_angle_other_deg1.01536918
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1285405
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.74627.681138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.30515540
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1150.2479
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023581
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02651
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.152.2791591
X-RAY DIFFRACTIONr_mcbond_other2.1412.2781590
X-RAY DIFFRACTIONr_mcangle_it3.2993.4041981
X-RAY DIFFRACTIONr_mcangle_other3.2993.4051982
X-RAY DIFFRACTIONr_scbond_it2.5462.51534
X-RAY DIFFRACTIONr_scbond_other2.5462.51534
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8353.652227
X-RAY DIFFRACTIONr_long_range_B_refined5.93128.6113618
X-RAY DIFFRACTIONr_long_range_B_other5.9328.6253619
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.557→1.597 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 80 -
Rwork0.207 3164 -
obs--87.3 %

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