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- PDB-1hd6: PHEROMONE ER-22, NMR -

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Basic information

Entry
Database: PDB / ID: 1hd6
TitlePHEROMONE ER-22, NMR
ComponentsPHEROMONE ER-22
KeywordsPHEROMONE
Function / homologyProtozoan pheromone superfamily / Pheromone, protozoan / Euplotes raikovi mating pheromone / pheromone activity / extracellular region / Mating pheromone Er-22
Function and homology information
Biological speciesEUPLOTES RAIKOVI (eukaryote)
MethodSOLUTION NMR / DISTANCE GEOMETRY, RESTRAINED ENERGY REFINEMENT
AuthorsLuginbuhl, P. / Liu, A. / Zerbe, O. / Ortenzi, C. / Luporini, P. / Wuthrich, K.
CitationJournal: J.Biomol.NMR / Year: 2001
Title: NMR Structure of the Pheromone Er-22 from Euplotes Raikovi
Authors: Liu, A. / Luginbuhl, P. / Zerbe, O. / Ortenzi, C. / Luporini, P. / Wuthrich, K.
History
DepositionNov 9, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 10, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHEROMONE ER-22


Theoretical massNumber of molelcules
Total (without water)3,9401
Polymers3,9401
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)20 / 50LOWEST RESIDUAL TARGET FUNCTION
RepresentativeModel #17

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Components

#1: Protein/peptide PHEROMONE ER-22


Mass: 3939.533 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) EUPLOTES RAIKOVI (eukaryote) / References: UniProt: P58548*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112QF-COSY
121TOCSY
1312Q-SPECTRUM
141E.COSY
15113C-HSQC
161NOESY
NMR detailsText: REPRESENTATIVE CONFORMER HAS THE SMALLEST RMSD TO THE MEAN STRUCTURE UPON SUPERPOSITION OF THE BACKBONE ATOMS N, CA, AND C' OF RESIDUES 2-32.

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Sample preparation

Sample conditionspH: 5 / Pressure: 1 atm / Temperature: 296 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX6001
Varian UNITYPLUSVarianUNITYPLUS7502

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Processing

NMR software
NameDeveloperClassification
OPALLUGINBUHL,GUNTERT,BILLETER,WUTHRICHrefinement
DIANAstructure solution
OPALstructure solution
RefinementMethod: DISTANCE GEOMETRY, RESTRAINED ENERGY REFINEMENT / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE. THREE-DIMENSIONAL STRUCTURE IN AQUEOUS SOLUTION REPRESENTED BY 20 CONFORMERS DETERMINED BY NUCLEAR MAGNETIC RESONANCE, DISTANCE ...Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE. THREE-DIMENSIONAL STRUCTURE IN AQUEOUS SOLUTION REPRESENTED BY 20 CONFORMERS DETERMINED BY NUCLEAR MAGNETIC RESONANCE, DISTANCE GEOMETRY AND RESTRAINED ENERGY REFINEMENT. DATA WERE COLLECTED AT 23 DEGREES CELSIUS AND AT PH 5.0. THEY CONSIST OF 497 UPPER LIMITS ON DISTANCES OBTAINED FROM NOE MEASUREMENTS AND 41 ANGLE CONSTRAINTS OBTAINED FROM NOE MEASUREMENTS AND COUPLING CONSTANT MEASUREMENTS. THESE INPUT DATA ARE ALSO AVAILABLE FROM THE PROTEIN DATA BANK. DISTANCE GEOMETRY CALCULATIONS WERE PERFORMED WITH THE PROGRAM DIANA (P. GUENTERT, W. BRAUN, K. WUTHRICH, J. MOL. BIOL. (1991) VOL. 217, 517 - 530). FOR THE RESTRAINED ENERGY MINIMIZATION THE PROGRAM OPAL (P. LUGINBUHL ET AL., J. BIOMOL. NMR (1996) VOL. 8, 136-146) WAS USED. FOR THE PRESENT STRUCTURES THE NMR DISTANCE CONSTRAINTS WERE WEIGHTED SUCH THAT A VIOLATION OF AN UPPER DISTANCE LIMIT OF 0.1 ANGSTROM CORRESPONDS TO AN ENERGY OF KT/2. THE CONSTRAINTS ON DIHEDRAL ANGLES RESULTING FROM MEASUREMENTS OF VICINAL COUPLING CONSTANTS WERE WEIGHTED SUCH THAT A VIOLATION OF 2.5 DEGREES CORRESPONDS TO AN ENERGY OF KT/2. DEPOSITED COORDINATES ARE THOSE OF CONFORMERS 1 - 20 IN THE PAPER CITED ON *JRNL* RECORDS ABOVE. NO VIOLATIONS OF DISTANCE CONSTRAINTS FROM NOES EXCEED 0.10 ANGSTROMS, AND NO VIOLATIONS OF ANGLE CONSTRAINTS EXCEED 2.5 DEGREES. ATOM NAMES HAVE BEEN ASSIGNED FOLLOWING THE RECOMMENDATIONS OF THE IUPAC-IUB COMMISSION AS PUBLISHED IN BIOCHEMISTRY (1970) VOL. 8, 3471 - 3479. THE INDIVIDUAL NUMBERS OF THE HYDROGEN ATOMS IN METHYL AND METHYLENE GROUPS ARE INDICATED AS THE FIRST CHARACTER RATHER THAN THE LAST CHARACTER OF THE ATOM NAMES. THE AVERAGE OF THE RMSD VALUES IN A PAIRWISE COMPARISON OF THE 20 NMR CONFORMERS TO THE MEAN STRUCTURE AS DESCRIBED IN THE PAPER CITED ON * JRNL* RECORDS ABOVE IS 0.47 ANGSTROMS FOR THE BACKBONE ATOMS OF RESIDUES 1 - 37, AND 0.75 ANGSTROMS FOR ALL HEAVY ATOMS. EXCLUDING THE CARBOXY-TERMINUS AND THE AMINO-TERMINUS, WHICH ARE LESS WELL DEFINED BY THE NMR DATA, THE AVERAGE OF THE RMSD VALUES IN A PAIRWISE COMPARISON TO THE MEAN STRUCTURE FOR RESIDUES 2 - 32 IS 0.27 ANGSTROMS FOR THE BACKBONE ATOMS.
NMR ensembleConformer selection criteria: LOWEST RESIDUAL TARGET FUNCTION
Conformers calculated total number: 50 / Conformers submitted total number: 20

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