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- PDB-2n3d: Atomic structure of the cytoskeletal bactofilin BacA revealed by ... -

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Basic information

Entry
Database: PDB / ID: 2n3d
TitleAtomic structure of the cytoskeletal bactofilin BacA revealed by solid-state NMR
ComponentsBactofilin A
KeywordsSTRUCTURAL PROTEIN / BacA / Bactofilin / cell shape / cytoskeleton / beta helix
Function / homologyBactofilin A/B / Polymer-forming cytoskeletal / Bactofilin A
Function and homology information
Biological speciesCaulobacter crescentus (bacteria)
MethodSOLID-STATE NMR / simulated annealing
AuthorsShi, C. / Fricke, P. / Lin, L. / Chevelkov, V. / Wegstroth, M. / Giller, K. / Becker, S. / Thanbichler, M. / Lange, A.
CitationJournal: Sci Adv / Year: 2015
Title: Atomic-resolution structure of cytoskeletal bactofilin by solid-state NMR.
Authors: Shi, C. / Fricke, P. / Lin, L. / Chevelkov, V. / Wegstroth, M. / Giller, K. / Becker, S. / Thanbichler, M. / Lange, A.
History
DepositionMay 29, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 6, 2016Group: Database references
Revision 1.2Feb 3, 2016Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bactofilin A


Theoretical massNumber of molelcules
Total (without water)19,3701
Polymers19,3701
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Bactofilin A


Mass: 19369.783 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter crescentus (bacteria) / Strain: ATCC 19089 / CB15 / Gene: bacA, CC_1873 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / References: UniProt: Q9A753

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111PDSD
1213D NCACX
1313D NCOCX
1413D NCOCA
1513D NCACO
162PDSD
172PDSD
183PDSD
193PDSD
11032D NHHC
21143D (H)CANH
21243D (H)CONH
21343D (H)CACO(N)H
21443D (H)COCA(N)H
21543D (H)CA(CO)NH
21644D HN(H)(H)NH

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Sample preparation

Details
Solution-IDContentsSolvent system
195 % [U-100% 13C; U-100% 15N] protein, 20 mM TRIS, 0.1 % DSS, 100% H2O100% H2O
295 % [2- 13C] Glycerol protein, 20 mM TRIS, 0.1 % DSS, 100% H2O100% H2O
395 % [1,3- 13C] Glycerol protein, 20 mM TRIS, 0.1 % DSS, 100% H2O100% H2O
495 % [U-100% 13C; U-100% 15N; U-100% 2H] protein, 50 mM TRIS, 0.1 % DSS, 0.5 mM EDTA, 1 mM DTT, 100% H2O100% H2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
95 %protein-1[U-100% 13C; U-100% 15N]1
20 mMTRIS-21
0.1 %DSS-41
95 %protein-5[2- 13C] Glycerol2
20 mMTRIS-62
0.1 %DSS-82
95 %protein-9[1,3- 13C] Glycerol3
20 mMTRIS-103
0.1 %DSS-123
95 %protein-13[U-100% 13C; U-100% 15N; U-100% 2H]4
50 mMTRIS-144
0.1 %DSS-164
0.5 mMEDTA-174
1 mMDTT-184
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
120 7.5 ambient 277 K
250 8.0 ambient 301 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7001
Bruker AvanceBrukerAVANCE8002
Bruker AvanceBrukerAVANCE9003
Bruker AvanceBrukerAVANCE8504

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Processing

NMR software
NameVersionDeveloperClassification
Sparky3.114Goddardchemical shift calculation
Sparky3.114Goddardchemical shift assignment
Sparky3.114Goddardpeak picking
CCPN2.4CCPNchemical shift calculation
CCPN2.4CCPNchemical shift assignment
CCPN2.4CCPNpeak picking
TopSpinBruker Biospinchemical shift calculation
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
X-PLOR NIH2.37Schwieters, Kuszewski, Tjandra and Clorechemical shift assignment
X-PLOR NIH2.37Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.37Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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