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- PDB-4ull: SOLUTION NMR STRUCTURE OF VEROTOXIN-1 B-SUBUNIT FROM E. COLI, 5 S... -

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Basic information

Entry
Database: PDB / ID: 4ull
TitleSOLUTION NMR STRUCTURE OF VEROTOXIN-1 B-SUBUNIT FROM E. COLI, 5 STRUCTURES
ComponentsShiga toxin 1B
KeywordsTOXIN
Function / homology
Function and homology information


modulation of host virulence by virus / hemolysis by symbiont of host erythrocytes / : / toxin activity / extracellular region
Similarity search - Function
OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #70 / Shiga-like toxin, beta subunit / Shiga-like toxin beta subunit / Enterotoxin / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Shiga-like toxin 1 subunit B / Shiga toxin 1B
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / SIMULATED ANNEALING, MOLECULAR DYNAMICS
AuthorsRichardson, J.M. / Evans, P.D. / Homans, S.W. / Donohue-Rolfe, A.
CitationJournal: Nat.Struct.Biol. / Year: 1997
Title: Solution structure of the carbohydrate-binding B-subunit homopentamer of verotoxin VT-1 from E. coli.
Authors: Richardson, J.M. / Evans, P.D. / Homans, S.W. / Donohue-Rolfe, A.
History
DepositionDec 17, 1996Processing site: BNL
Revision 1.0Apr 1, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 11, 2019Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_nat / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref / struct_ref_seq
Item: _entity.pdbx_description / _entity_src_nat.common_name ..._entity.pdbx_description / _entity_src_nat.common_name / _entity_src_nat.pdbx_beg_seq_num / _entity_src_nat.pdbx_end_seq_num / _entity_src_nat.pdbx_ncbi_taxonomy_id / _entity_src_nat.pdbx_organism_scientific / _entity_src_nat.strain / _pdbx_database_status.process_site / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Shiga toxin 1B


Theoretical massNumber of molelcules
Total (without water)7,6991
Polymers7,6991
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)5 / 40NO RESTRAINT VIOLATIONS ABOVE 0.7 ANGSTROM
Representative

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Components

#1: Protein Shiga toxin 1B


Mass: 7698.634 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Genus: , Lambda-like viruses / Species: , / References: UniProt: Q8G8Y6, UniProt: P69179*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111ASSIGNMENT HNCO
121HCACO
131HN(CO)CA
1413D TOCSY. 1H-1H DISTANCE DERIVATION; 3D-NOESY
NMR detailsText: THE STRUCTURE WAS DETERMINED BY TRIPLE-RESONANCE NMR SPECTROSCOPY ON UNIFORMLY 13C, 15N-LABELED VEROTOXIN-1. IONIC_STRENGTH: 200 MM PRESSURE: ATMOSPHERIC SOLVENT SYSTEM: H20

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Sample preparation

Sample conditionspH: 7 / Temperature: 318 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 500.3 MHz

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
NMR software
NameVersionDeveloperClassification
X-PLORBRUNGERrefinement
XPLOR3.1structure solution
RefinementMethod: SIMULATED ANNEALING, MOLECULAR DYNAMICS / Software ordinal: 1
NMR ensembleConformer selection criteria: NO RESTRAINT VIOLATIONS ABOVE 0.7 ANGSTROM
Conformers calculated total number: 40 / Conformers submitted total number: 5

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