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- PDB-2lqm: Solution Structures of RadA intein from Pyrococcus horikoshii -

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Basic information

Entry
Database: PDB / ID: 2lqm
TitleSolution Structures of RadA intein from Pyrococcus horikoshii
ComponentsPho radA intein
KeywordsUNKNOWN FUNCTION
Function / homology
Function and homology information


intein-mediated protein splicing / ATP-dependent DNA damage sensor activity / DNA recombination / damaged DNA binding / DNA repair / ATP binding
Similarity search - Function
Endonuclease - Pi-scei; Chain A, domain 1 / Hedgehog/Intein (Hint) domain / DNA recombination/repair protein RadA / Intein splicing domain / DNA recombination and repair protein Rad51-like, C-terminal / Intein C-terminal splicing region / Rad51 / Intein C-terminal splicing motif profile. / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region ...Endonuclease - Pi-scei; Chain A, domain 1 / Hedgehog/Intein (Hint) domain / DNA recombination/repair protein RadA / Intein splicing domain / DNA recombination and repair protein Rad51-like, C-terminal / Intein C-terminal splicing region / Rad51 / Intein C-terminal splicing motif profile. / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / 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 / DNA recombination and repair protein RecA, monomer-monomer interface / RecA family profile 2. / DNA recombination and repair protein RecA-like, ATP-binding domain / RecA family profile 1. / DNA repair Rad51/transcription factor NusA, alpha-helical / Helix-hairpin-helix domain / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / Beta Complex / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
DNA repair and recombination protein RadA
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model 1
AuthorsOeemig, J.S. / Zhou, D. / Kajander, T. / Wlodawer, A. / Iwai, H.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: NMR and Crystal Structures of the Pyrococcus horikoshii RadA Intein Guide a Strategy for Engineering a Highly Efficient and Promiscuous Intein.
Authors: Oeemig, J.S. / Zhou, D. / Kajander, T. / Wlodawer, A. / Iwai, H.
History
DepositionMar 9, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2012Group: Database references
Revision 1.2Jun 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 1.3May 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: Pho radA intein


Theoretical massNumber of molelcules
Total (without water)19,9191
Polymers19,9191
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 / 100target function
RepresentativeModel #1closest to the average

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Components

#1: Protein Pho radA intein / DNA repair and recombination protein radA


Mass: 19918.551 Da / Num. of mol.: 1 / Mutation: C1A, T173A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea)
Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3
Gene: DNA repair and recombination protein RadA, PH0263, radA
Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: O58001

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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-15N HSQC
1312D 1H-13C HSQC aliphatic
1412D 1H-13C HSQC aromatic
1513D CBCA(CO)NH
1613D C(CO)NH
1713D HNCO
1813D HNCA
1913D HN(CA)CB
11013D HBHA(CO)NH
11113D HN(CO)CA
11213D HNHB
11313D 1H-15N TOCSY
11413D HCACO
11513D 1H-13C NOESY aliphatic
11613D 1H-15N NOESY
11713D (H)CCH-COSY
11813D (H)CCH-TOCSY
1191intraHNCA
1201(HB)CB(CGCD)HD
1211(HB)CB(CGCDCE)HE

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Sample preparation

DetailsContents: 0.4 mM [U-99% 13C; U-99% 15N] PhoRadA intein, 20 mM sodium phosphate, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMPhoRadA intein-1[U-99% 13C; U-99% 15N]1
20 mMpotassium phosphate-21
Sample conditionspH: 6 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
Amber11Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmrefinement
VnmrJ2.2Variancollection
NMRPipe5Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
CINGGeerten W. Vuisterstructure validation
CCPNMR2.2CCPNdata analysis
TALOSTALOS+Cornilescu, Delaglio and Baxdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 3515 / NOE intraresidue total count: 688 / NOE long range total count: 1436 / NOE medium range total count: 425 / NOE sequential total count: 966 / Protein phi angle constraints total count: 136 / Protein psi angle constraints total count: 144
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 12.26 ° / Maximum upper distance constraint violation: 0.67 Å
NMR ensemble rmsDistance rms dev: 0.0152 Å / Distance rms dev error: 0.0024 Å

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