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- PDB-1qtg: AVERAGED NMR MODEL OF SWITCH ARC, A DOUBLE MUTANT OF ARC REPRESSOR -

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Basic information

Entry
Database: PDB / ID: 1qtg
TitleAVERAGED NMR MODEL OF SWITCH ARC, A DOUBLE MUTANT OF ARC REPRESSOR
ComponentsTranscriptional repressor arc
KeywordsGENE REGULATION / BETA-SHEET / RIGHT-HANDED HELIX / STRUCTURAL CHANGE
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Arc-like DNA binding domain / Arc-like DNA binding domain / Met repressor-like / Arc Repressor Mutant / Arc-type ribbon-helix-helix / Ribbon-helix-helix / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcriptional repressor arc
Similarity search - Component
Biological speciesLederbergvirus P22
MethodSOLUTION NMR / simulated annealing
AuthorsCordes, M.H.J. / Walsh, N.P. / McKnight, C.J. / Sauer, R.T.
CitationJournal: Science / Year: 1999
Title: Evolution of a protein fold in vitro.
Authors: Cordes, M.H. / Walsh, N.P. / McKnight, C.J. / Sauer, R.T.
History
DepositionJun 27, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Dec 21, 2022Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / struct_ref / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_src_gen.pdbx_beg_seq_num ..._entity.pdbx_description / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_seq_db_seq_num
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional repressor arc
B: Transcriptional repressor arc


Theoretical massNumber of molelcules
Total (without water)12,4772
Polymers12,4772
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)1 / -
Representative

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Components

#1: Protein Transcriptional repressor arc


Mass: 6238.272 Da / Num. of mol.: 2 / Mutation: N11L, L12N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lederbergvirus P22 / Genus: P22-like viruses / Description: MUTATED SYNTHETIC ARC GENE / Gene: arc / Plasmid: PET800-SWITCH_ARC / Production host: Escherichia coli (E. coli) / References: UniProt: P03050

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

Radiation wavelengthRelative weight: 1

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Processing

RefinementMethod: simulated annealing / Software ordinal: 1
Details: GENERATION OF THIS MODEL OF THE SWITCH ARC MUTANT INVOLVED A COMBINATION OF EXPERIMENTAL AND SIMU LATED DISTANCE RESTRAINTS. FOR RESIDUES 7-14, 81 NOE CROSSPEAKS WERE OBTAINED FROM A 50-MS ...Details: GENERATION OF THIS MODEL OF THE SWITCH ARC MUTANT INVOLVED A COMBINATION OF EXPERIMENTAL AND SIMU LATED DISTANCE RESTRAINTS. FOR RESIDUES 7-14, 81 NOE CROSSPEAKS WERE OBTAINED FROM A 50-MS 2D NOES Y SPECTRUM AND WERE TRANSLATED INTO STRONG (1.8-2.8 A), MEDIUM (1.8-3.3 A), MEDIUM-WEAK (1.8-3.8 A ) AND WEAK (1.8-4.3 A) DISTANCE RESTRAINTS.18 ADDITIONAL CROSSPEAKS WERE OBTAINED FROM A 150-MS 3D NOESY SPECTRUM AND WERE ASSIGNED LOOSER RESTRAINTS (1.8 TO 4.0 A OR 1.8 TO 6.0 A)BECAUSE OF THE L ONGER MIXING TIME USED IN THIS EXPERIMENT. TO SIMULATE THE STRUCTURE OF RESIDUES 14 TO 53 (RESIDUE 14 WAS DESCRIBED BY BOTH ACTUAL AND COMPUTED RESTRAINTS), A LIST OF 1635 DISTANCES WAS GENERATED BETWEEN PAIRS OF HEAVY ATOMS WITHIN 4 A OF EACH OTHER IN THE WILD-TYPE ARC CRYSTAL STRUCTURE, AND THE INTERATOMIC DISTANCES WERE CONSTRAINED TO BE WITHIN + OR - 1.0 A OF THIS VALUE. 28 INITIAL STR UCTURES WITH RANDOM CONFIGURATIONS FOR RESIDUES 1 TO 13 WERE GENERATED BY PERFORMING A SET OF CALC ULATIONS WITH ONLY THE SIMULATED RESTRAINTS FOR RESIDUES 14 TO 53. THEN, 28 MODEL STRUCTURES WERE GENERATED BY INCLUDING THE EXPERIMENTAL RESTRAINTS FOR RESIDUES 7 TO 14. NO RESTRAINTS WERE USED F OR RESIDUES 1 TO 6, WHICH APPEAR TO BE DISORDERED. AMBIGUITIES IN INTRA- AND INTERMOLECULAR NOE AS SIGNMENT RESULTING FROM ARC'S TWOFOLD SYMMETRY WERE RESOLVED COMPUTATIONALLY AS DESCRIBED (M. NILG ES, PROTEIN STRUCT. FUNCT. GENET. 17, 297 (1993).19 OF 28 STRUCTURES WERE ACCEPTED WITH NO NOE VIO LATIONS GREATER THAN 0.3 A. THE FIVE STRUCTURES WITH THE HIGHEST ENERGY, WHICH ALSO CONTAINED BACK BONE DIHEDRAL ANGLES IN DISALLOWED REGIONS OF RAMACHANDRAN SPACE, WERE DISCARDED. THE REMAINING 14 STRUCTURES, WHICH HAD PAIRWISE RMSD'S OF 0.6 A (BACKBONE) AND 1.6 A (HEAVY), WERE USED TO GENERAT E A MINIMIZED AVERAGE MODEL.
NMR ensembleConformers submitted total number: 1

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