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- PDB-1tnt: A NOVEL CLASS OF WINGED HELIX-TURN-HELIX PROTEIN: THE DNA-BINDING... -

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Basic information

Entry
Database: PDB / ID: 1tnt
TitleA NOVEL CLASS OF WINGED HELIX-TURN-HELIX PROTEIN: THE DNA-BINDING DOMAIN OF MU TRANSPOSASE
ComponentsMU-TRANSPOSASE
KeywordsDNA BINDING PROTEIN / DNA-BINDING PROTEIN
Function / homology
Function and homology information


Ligases; Forming phosphoric-ester bonds / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 3'-phosphomonoesters / latency-replication decision / transposase activity / DNA transposition / double-stranded DNA endonuclease activity / viral DNA genome replication / ligase activity / DNA integration / DNA replication ...Ligases; Forming phosphoric-ester bonds / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 3'-phosphomonoesters / latency-replication decision / transposase activity / DNA transposition / double-stranded DNA endonuclease activity / viral DNA genome replication / ligase activity / DNA integration / DNA replication / host cell cytoplasm / DNA repair / DNA binding / metal ion binding
Similarity search - Function
Bacteriophage Mu, transposase / Transposase, Mu, C-terminal / Mu DNA binding, I gamma subdomain / Transposase-like, Mu, C-terminal / Bacteriophage Mu transposase / Mu DNA binding, I gamma subdomain / Mu transposase, C-terminal / Mu-type HTH domain / Mu DNA-binding domain / Mu-type HTH domain profile. ...Bacteriophage Mu, transposase / Transposase, Mu, C-terminal / Mu DNA binding, I gamma subdomain / Transposase-like, Mu, C-terminal / Bacteriophage Mu transposase / Mu DNA binding, I gamma subdomain / Mu transposase, C-terminal / Mu-type HTH domain / Mu DNA-binding domain / Mu-type HTH domain profile. / Putative DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesEnterobacteria phage Mu (virus)
MethodSOLUTION NMR
AuthorsClore, G.M. / Clubb, R.T. / Omichinski, J.G. / Gronenborn, A.M.
CitationJournal: Structure / Year: 1994
Title: A novel class of winged helix-turn-helix protein: the DNA-binding domain of Mu transposase.
Authors: Clubb, R.T. / Omichinski, J.G. / Savilahti, H. / Mizuuchi, K. / Gronenborn, A.M. / Clore, G.M.
History
DepositionOct 10, 1994Processing site: BNL
Revision 1.0Feb 14, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Structure summary
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_keywords / 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.process_site / _struct_keywords.text / _struct_ref_seq_dif.details
Revision 1.4May 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: MU-TRANSPOSASE


Theoretical massNumber of molelcules
Total (without water)8,2691
Polymers8,2691
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)33 / -
Representative

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Components

#1: Protein MU-TRANSPOSASE


Mass: 8268.502 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage Mu (virus) / Genus: Mu-like viruses / References: UniProt: P07636

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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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Processing

RefinementSoftware ordinal: 1
Details: THE 3D SOLUTION STRUCTURE OF THE DNA BINDING DOMAIN OF MU TRANSPOSASE (MUA76, RESIDUES 1 - 76) WAS SOLVED BY MULTIDIMENSIONAL HETERONUCLEAR-EDITED NMR EXPERIMENTS AND IS BASED ON 1320 ...Details: THE 3D SOLUTION STRUCTURE OF THE DNA BINDING DOMAIN OF MU TRANSPOSASE (MUA76, RESIDUES 1 - 76) WAS SOLVED BY MULTIDIMENSIONAL HETERONUCLEAR-EDITED NMR EXPERIMENTS AND IS BASED ON 1320 EXPERIMENTAL RESTRAINTS COMPRISING THE FOLLOWING: (A) 1192 APPROXIMATE INTERPROTON DISTANCE RESTRAINTS (308 SEQUENTIAL, 266 SHORT RANGE 1 , |I-J| <=5, 323 LONG RANGE |I-J|>5, AND 295 INTRARESIDUE (B) 18 DISTANCE RESTRAINTS FOR 9 BACKBONE HYDROGEN BONDS (C) 36 HN-CAH COUPLING CONSTANT RESTRAINTS (D) 74 TORSION ANGLE RESTRAINTS (40 PHI, 23 CHI1 AND 11 CHI2). A COMPLETE LIST OF EXPERIMENTAL RESTRAINTS HAVE BEEN DEPOSITED WITH THE BROOKHAVEN DATA BANK. THE STRUCTURES ARE CALCULATED USING THE HYBRID METRIC MATRIX DISTANCE GEOMETRY-DYNAMICAL SIMULATED ANNEALING METHOD DESCRIBED BY: NILGES, M., CLORE, G.M. & GRONENBORN, A.M. (1988) FEBS LETT 229, 317 - 324 ALL STRUCTURAL STATISTICS ARE GIVEN IN REF. 1. PDB ENTRY 1TNS IS THE RESTRAINED MINIMIZED AVERAGE STRUCTURE: (SA)R. THIS IS OBTAINED BY FIRST AVERAGING THE COORDINATES OF THE INDIVIDUAL 33 DYNAMICAL SIMULATED ANNEALING (SA) STRUCTURES BEST FITTED TO RESIDUES 3 - 36 AND 45 - 65 AND SUBJECTING THE RESULTING COORDINATES TO RESTRAINED MINIMIZATION. THE LAST NUMBER COLUMN IN THIS SET OF COORDINATES (THE B-FACTOR COLUMN IN X-RAY STRUCTURES) GIVES THE AVERAGE RMS DIFFERENCE BETWEEN THE INDIVIDUAL SA STRUCTURES AND THE MEAN STRUCTURE. THE NUMBERS IN THE LAST COLUMN OF THE INDIVIDUAL STRUCTURES HAVE NO MEANING. RESIDUES 1 - 2, 66 - 76, AND 37 - 44 ARE DISORDERED IN SOLUTION. THIS ENTRY CONTAINS THE 33 INDIVIDUAL STRUCTURES.
NMR ensembleConformers submitted total number: 33

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