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- PDB-2ezi: SOLUTION NMR STRUCTURE OF THE IGAMMA SUBDOMAIN OF THE MU END DNA ... -

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Basic information

Entry
Database: PDB / ID: 2ezi
TitleSOLUTION NMR STRUCTURE OF THE IGAMMA SUBDOMAIN OF THE MU END DNA BINDING DOMAIN OF MU PHAGE TRANSPOSASE, 30 STRUCTURES
ComponentsTRANSPOSASE
KeywordsDNA BINDING PROTEIN / DNA-BINDING PROTEIN / TRANSPOSITION
Function / homology
Function and homology information


Ligases; Forming phosphoric-ester bonds / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 3'-phosphomonoesters / double-stranded DNA endonuclease activity / latency-replication decision / transposase activity / DNA transposition / viral DNA genome replication / ligase activity / DNA integration / host cell cytoplasm ...Ligases; Forming phosphoric-ester bonds / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 3'-phosphomonoesters / double-stranded DNA endonuclease activity / latency-replication decision / transposase activity / DNA transposition / viral DNA genome replication / ligase activity / DNA integration / host cell cytoplasm / DNA replication / 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 / Homeodomain-like / 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 / simulated annealing
AuthorsClore, G.M. / Clubb, R.T. / Schumaker, S. / Gronenborn, A.M.
CitationJournal: J.Mol.Biol. / Year: 1997
Title: Solution structure of the I gamma subdomain of the Mu end DNA-binding domain of phage Mu transposase.
Authors: Clubb, R.T. / Schumacher, S. / Mizuuchi, K. / Gronenborn, A.M. / Clore, G.M.
History
DepositionJul 25, 1997Processing site: BNL
Revision 1.0Dec 3, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRANSPOSASE


Theoretical massNumber of molelcules
Total (without water)8,8801
Polymers8,8801
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)30 / -
Representative

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Components

#1: Protein TRANSPOSASE /


Mass: 8880.119 Da / Num. of mol.: 1 / Fragment: IGAMMA SUBDOMAIN, RESIDUES 174 - 247 / Source method: isolated from a natural source / Details: MUA OF PHAGE MU TRANSPOSASE / Source: (natural) 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

Sample conditionspH: 6.3 / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMX500BrukerAMX5005001
Bruker AMX600BrukerAMX6006002

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionClassification
X-PLOR (SEE ABOVE)ABOVE)structure solution
X-PLOR (SEE ABOVE)ABOVE)refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: THE 3D STRUCTURE OF THE IGAMMA SUBDOMAIN OF MU A TRANSPOSASE WAS SOLVED BY MULTI-DIMENSIONAL HETERONUCLEAR NMR AND IS BASED ON 1293 EXPERIMENTAL NMR RESTRAINTS: 264 SEQUENTIAL (|I- J|=1), ...Details: THE 3D STRUCTURE OF THE IGAMMA SUBDOMAIN OF MU A TRANSPOSASE WAS SOLVED BY MULTI-DIMENSIONAL HETERONUCLEAR NMR AND IS BASED ON 1293 EXPERIMENTAL NMR RESTRAINTS: 264 SEQUENTIAL (|I- J|=1), 282 MEDIUM RANGE (1 < |I-J| <=5) AND 178 LONG RANGE (|I-J| >5) INTERRESIDUES AND 245 INTRARESIDUE APPROXIMATE INTERPROTON DISTANCE RESTRAINTS; 40 DISTANCE RESTRAINTS FOR 20 BACKBONE H-BONDS; 108 TORSION ANGLE RESTRAINTS; 47 THREE-BOND HN-HA COUPLING CONSTANT RESTRAINTS; AND 129 (66 CALPHA AND 63 CBETA) 13C SHIFT RESTRAINTS. THE STRUCTURES WERE CALCULATED USING THE SIMULATED ANNEALING PROTOCOL OF NILGES ET AL. (1988) FEBS LETT. 229, 129-136 USING THE PROGRAM X-PLOR 3.1 (BRUNGER) MODIFIED TO INCORPORATE COUPLING CONSTANT (GARRETT ET AL. (1984) J. MAGN. RESON. SERIES B 104, 99-103) AND CARBON CHEMICAL SHIFT (KUSZEWSKI ET AL. (1995) J. MAGN. RESON. SERIES B 106, 92-96) RESTRAINTS, AND A CONFORMATIONAL DATABASE POTENTIAL (KUSZEWSKI ET AL. (1996) PROTEIN SCI. 5, 1067-1080; KUSZEWSKI ET AL. (1997) J. MAGN. RESON 125, 171-177). THE RESTRAINED REGULARIZED MEAN STRUCTURE IS PRESENTED IN ENTRY 2EZH AND 30 STRUCTURES ARE PRESENTED IN ENTRY 2EZI, AND THE EXPERIMENTAL RESTRAINTS IN 2EZHMR. IN THE RESTRAINED REGULARIZED MEAN COORDINATES (2EZH) THE LAST COLUMN REPRESENTS THE AVERAGE RMS DIFFERENCE BETWEEN THE INDIVIDUAL SIMULATED ANNEALING STRUCTURES AND THE MEAN COORDINATE POSITIONS. THE LAST COLUMN IN THE INDIVIDUAL SA STRUCTURES (2EZI) HAS NO MEANING. BEST FITTING TO GENERATE THE AVERAGE STRUCTURE IS WITH RESPECT TO RESIDUES 180 - 240. NOTE THAT THE OCCUPANCY FIELD HAS NO MEANING.
NMR ensembleConformers submitted total number: 30

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