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- PDB-2lwy: Solution Structure of Bacterial Intein-Like domain from Clostridi... -

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Basic information

Entry
Database: PDB / ID: 2lwy
TitleSolution Structure of Bacterial Intein-Like domain from Clostridium thermocellum
ComponentsBACTERIAL INTEIN-LIKE DOMAIN
KeywordsUNKNOWN FUNCTION / BIL / CthBIL4 / Bacterial Intein-Like / HINT
Function / homology
Function and homology information


intein-mediated protein splicing / membrane => GO:0016020
Similarity search - Function
WHH domain-containing protein / A nuclease of the HNH/ENDO VII superfamily with conserved WHH / Endonuclease - Pi-scei; Chain A, domain 1 / Hedgehog/Intein (Hint) domain / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region ...WHH domain-containing protein / A nuclease of the HNH/ENDO VII superfamily with conserved WHH / Endonuclease - Pi-scei; Chain A, domain 1 / Hedgehog/Intein (Hint) domain / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / Hint domain superfamily / Beta Complex / Mainly Beta
Similarity search - Domain/homology
INTEIN_C_TER domain-containing protein
Similarity search - Component
Biological speciesClostridium thermocellum (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsAranko, A.S. / Oeemig, J.S. / Iwai, H.
CitationJournal: Febs J. / Year: 2013
Title: Structural basis for protein trans-splicing by a bacterial intein-like domain - protein ligation without nucleophilic side chains.
Authors: Aranko, A.S. / Oeemig, J.S. / Iwai, H.
History
DepositionAug 9, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Jul 17, 2013Group: 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 / 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 / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BACTERIAL INTEIN-LIKE DOMAIN


Theoretical massNumber of molelcules
Total (without water)15,2971
Polymers15,2971
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1closest to the average

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Components

#1: Protein BACTERIAL INTEIN-LIKE DOMAIN


Mass: 15297.482 Da / Num. of mol.: 1 / Mutation: C1A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium thermocellum (bacteria) / Strain: ATCC 27405 / DSM 1237 / Gene: Cthe_2047 / Plasmid: pSCFRSF17 / Production host: Escherichia coli (E. coli) / References: UniProt: A3DH25

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1312D 1H-13C HSQC aromatic
1413D CBCA(CO)NH
1513D C(CO)NH
1613D HNCO
1713D HN(CA)CB
1813D HBHA(CO)NH
1913D (H)CCH-TOCSY
11013D (H)CCH-COSY
11112D 1H-15N HSQC
11213D HN(CA)CO
11313D 1H-15N TOCSY
11413D 1H-15N NOESY
11513D 1H-13C NOESY aliphatic

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Sample preparation

DetailsContents: 1.2 mM [U-99% 13C; U-99% 15N] CthBIL4, 20 mM potassium phosphate, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMCthBIL4-1[U-99% 13C; U-99% 15N]1
20 mMpotassium phosphate-21
Sample conditionspH: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CINGGeerten W. Vuisterstructure validation
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
VnmrJVariancollection
CCPNMRCCPNchemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 3735 / NOE intraresidue total count: 766 / NOE long range total count: 1608 / NOE medium range total count: 465 / NOE sequential total count: 896
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum upper distance constraint violation: 0.35 Å
NMR ensemble rmsDistance rms dev: 0.0068 Å / Distance rms dev error: 0.003 Å

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