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- PDB-1ner: SOLUTION STRUCTURE OF THE MU NER PROTEIN BY MULTIDIMENSIONAL NMR -

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Basic information

Entry
Database: PDB / ID: 1ner
TitleSOLUTION STRUCTURE OF THE MU NER PROTEIN BY MULTIDIMENSIONAL NMR
ComponentsDNA-BINDING PROTEIN NER
KeywordsDNA BINDING PROTEIN / DNA-BINDING PROTEIN
Function / homology
Function and homology information


transcription repressor complex / host cell cytoplasm / DNA binding
Similarity search - Function
Ner, winged helix-turn-helix DNA-binding domain / Winged helix-turn-helix DNA-binding / lambda repressor-like DNA-binding domains / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Negative regulator of transcription
Similarity search - Component
Biological speciesEnterobacteria phage Mu (virus)
MethodSOLUTION NMR
AuthorsClore, G.M. / Strzelecka, T.E. / Gronenborn, A.M.
Citation
Journal: Structure / Year: 1995
Title: The solution structure of the Mu Ner protein reveals a helix-turn-helix DNA recognition motif.
Authors: Strzelecka, T.E. / Clore, G.M. / Gronenborn, A.M.
#1: Journal: Biochemistry / Year: 1989
Title: Determination of the Secondary Structure of the DNA Binding Protein Ner from Phage Mu Using 1H Homonuclear and 15N-1H Heteronuclear NMR Spectroscopy
Authors: Gronenborn, A.M. / Wingfield, P.T. / Clore, G.M.
History
DepositionAug 24, 1995Processing site: BNL
Revision 1.0Dec 7, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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
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: DNA-BINDING PROTEIN NER


Theoretical massNumber of molelcules
Total (without water)8,3891
Polymers8,3891
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)30 / -
Representative

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Components

#1: Protein DNA-BINDING PROTEIN NER


Mass: 8388.538 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage Mu (virus) / Genus: Mu-like viruses / References: UniProt: P06020

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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

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
NMR softwareName: X-PLOR / Developer: BRUNGER / Classification: refinement
RefinementSoftware ordinal: 1
Details: THE 3D STRUCTURE OF THE MU NER PROTEIN BY MULTI-DIMENSIONAL HETERONUCLEAR NMR IS BASED ON 1546 EXPERIMENTAL RESTRAINTS COMPRISING THE FOLLOWING: 944 INTERPROTON DISTANCE RESTRAINTS [251 ...Details: THE 3D STRUCTURE OF THE MU NER PROTEIN BY MULTI-DIMENSIONAL HETERONUCLEAR NMR IS BASED ON 1546 EXPERIMENTAL RESTRAINTS COMPRISING THE FOLLOWING: 944 INTERPROTON DISTANCE RESTRAINTS [251 SEQUENTIAL; 202 SHORT RANGE (1<|I-J|<=5; 157 LONG RANGE (|I-J|>5); AND 334 INTRARESIDUE]; 40 DISTANCE RESTRAINTS FOR 20 BACKBONE HYDROGEN BONDS; 89 TORSION ANGLE RESTRAINTS 56 PHI, 27 CH1 AND 6 CHI2); 46 3 BOND HN-HA COUPLING CONSTANTS; 140 SECONDARY 13C SHIFTS (72 CA AND 68 CB); 287 1H CHEMICAL SHIFTS (74 HA, 39 METHYL AND 174 OTHER, WITH NO EXCHANGEABLE PROTON SHIFTS). THE STRUCTURE WAS DETERMINED BY SIMULATED ANNEALING [NILGES, CLORE AND GRONENBORN (1988) FEBS LETT. 229, 317 - 324] USING THE PROGRAM X-PLOR (BRUNGER) MODIFIED TO INCORPORATE COUPLING CONSTANT [GARRETT ET AL. AND CLORE (1994) J. MAGN. RESON. B104, 99 - 103], CARBON CHEMICAL SHIFT [KUSZEWSKI, QIN, GRONENBORN AND CLORE (1995) J. MAGN. RESON. B106, 92 - 96] AND PROTON CHEMICAL SHIFT [KUSZEWSKI, GRONENBORN AND CLORE (1995) J. MAGN. RESON. B107, 293 - 297] RESTRAINTS. ENTRY 1NEQ IS THE RESTRAINED REGULARIZED MEAN STRUCTURE OBTAINED BY AVERAGING THE COORDINATES OF THE 30 SIMULATED ANNEALING STRUCTURES BEST FITTED TO EACH OTHER (RESIDUES 8 - 66). THE N- AND C-TERMINI ARE DISORDERED, AND THE NUMBER IN THE LAST COLUMN (THE B- FACTOR COLUMN) GIVES THE AVERAGE RMS TO THE MEAN COORDINATE POSITIONS.
NMR ensembleConformers submitted total number: 30

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