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- PDB-1dcj: SOLUTION STRUCTURE OF YHHP, A NOVEL ESCHERICHIA COLI PROTEIN IMPL... -

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Basic information

Entry
Database: PDB / ID: 1dcj
TitleSOLUTION STRUCTURE OF YHHP, A NOVEL ESCHERICHIA COLI PROTEIN IMPLICATED IN THE CELL DIVISION
ComponentsYHHP PROTEIN
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / ALPHA-BETA SANDWICH
Function / homology
Function and homology information


sulfur carrier activity / tRNA wobble position uridine thiolation / Mo-molybdopterin cofactor biosynthetic process / cytosol
Similarity search - Function
Sulfur carrier protein TusA / TusA-like domain / Uncharacterized protein family UPF0033 signature. / TusA-like domain / Sulfurtransferase TusA / TusA-like domain superfamily / Translation Initiation Factor IF3 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Sulfur carrier protein TusA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / HYBRID DISTANCE GEOMETRY-SIMULATED ANNEALING
AuthorsKatoh, E. / Hatta, T. / Shindo, H. / Mizuno, T. / Yamazaki, T.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: High precision NMR structure of YhhP, a novel Escherichia coli protein implicated in cell division.
Authors: Katoh, E. / Hatta, T. / Shindo, H. / Ishii, Y. / Yamada, H. / Mizuno, T. / Yamazaki, T.
#1: Journal: J.Bacteriol. / Year: 1998
Title: The yhhP Gene Encoding a Small Ubiquitous Protein is Fundamental for Normal Cell Growth of Escherichia Coli
Authors: Yamashino, T. / Isomura, M. / Ueguchi, C. / Mizuno, T.
#2: Journal: To be Published
Title: Characterization of the yhhP Gene Whose Deficiency Results in a Non-Divided Filamentous Cell Morphology in Escherichia coli
Authors: Ishii, Y. / Yamada, H. / Yamazaki, T. / Katoh, E. / Mizuno, T.
History
DepositionNov 5, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: YHHP PROTEIN


Theoretical massNumber of molelcules
Total (without water)9,1061
Polymers9,1061
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)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein YHHP PROTEIN


Mass: 9105.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET21 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A890

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-SEPARATED NOESY
121HNHA
131HNHB
1434D 13C-SEPARATED NOESY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY.

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Sample preparation

Details
Solution-IDContents
11MM YHHP U-15N; 10MM PHOSPHATE BUFFER K; 100MM NACL; 2MM NAN3; 2MM DTT; 90% H20, 10% D2O
21MM YHHP U-15N, 13C; 10MM PHOSPHATE BUFFER K; 100MM NACL; 2MM NAN3; 2MM DTT; 90% H20, 10% D2O
31MM YHHP U-15N, 13C; 10MM PHOSPHATE BUFFER K; 100MM NACL; 2MM NAN3; 2MM DTT; 100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1100mM NACL 7.1 AMBIENT 298 K
2100mM NACL 7.1 AMBIENT 298 K
3100mM NACL 7.1 AMBIENT 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 750 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMRBRUKERcollection
NMRPipeDELAGLIOprocessing
CAPP/PIPP/STAPPGARRETTdata analysis
X-PLOR3.1BRUNGERstructure solution
X-PLOR3.1BRUNGERrefinement
RefinementMethod: HYBRID DISTANCE GEOMETRY-SIMULATED ANNEALING / Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON A TOTAL OF 1655 RESTRAINTS, 1390 ARE NOE-DERIVED DISTANCE CONSTRAINTS, 211 DIHEDRAL ANGLE RESTRAINTS, 54 DISTANCE RESTRAINTS FROM HYDROGEN BONDS.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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