Journal: J.Mol.Biol. / Year: 2005 Title: Visualization of the Phosphorylated Active Site Loop of the Cytoplasmic B Domain of the Mannitol Transporter II(Mannitol) of the Escherichia coli Phosphotransferase System by NMR Spectroscopy ...Title: Visualization of the Phosphorylated Active Site Loop of the Cytoplasmic B Domain of the Mannitol Transporter II(Mannitol) of the Escherichia coli Phosphotransferase System by NMR Spectroscopy and Residual Dipolar Couplings. Authors: Suh, J.Y. / Tang, C. / Cai, M. / Clore, G.M.
History
Deposition
Jun 17, 2005
Deposition site: RCSB / Processing site: RCSB
Revision 1.0
Nov 22, 2005
Provider: repository / Type: Initial release
Revision 1.1
Apr 27, 2008
Group: Version format compliance
Revision 1.2
Jul 13, 2011
Group: Source and taxonomy / Version format compliance
Method: torsion angle dynamics / Software ordinal: 1 Details: THE TARGET FUNCTION COMPRISES TERMS FOR THE NOE-DERIVED INTERPROTON DISTANCE RESTRAINTS, TORSION ANGLE RESTRAINTS, AND RESIDUAL DIPOLAR COUPLINGS (N-H, N-C' AND HN-C') IN THREE ALIGNMENT ...Details: THE TARGET FUNCTION COMPRISES TERMS FOR THE NOE-DERIVED INTERPROTON DISTANCE RESTRAINTS, TORSION ANGLE RESTRAINTS, AND RESIDUAL DIPOLAR COUPLINGS (N-H, N-C' AND HN-C') IN THREE ALIGNMENT MEDIA; A QUARTIC VAN DE WAALS REPULSION TERM, AND A TORSION ANGLE DATABASE POTENTIAL OF MEAN FORCE. IN THIS ENTRY THE LAST COLUMN FOR FOR THE ACTIVE SITE LOOP (RESIDUES 383-393) REPRESENTS THE AVERAGE RMS DIFFERENCE BETWEEN THE INDIVIDUAL 150 SIMULATED ANNEALING STRUCTURES AND THE MEAN COORDINATE POSITIONS. NOTE ONLY THE COORDINATES OF THE ACTIVE SITE LOOP (RESIDUES 383-393) HAVE BEEN REFINED; THE REMAINDER OF THE PROTEIN COORDINATES ARE HELD FIXED AT THEIR POSITIONS IN UNPHOSPHORYLATED IIBMTL (PDB ACCESSION CODE 1VKR). THE LAST COLUMN FOR RESIDUES OUTSIDE THE ACTIVE SITE REPRESENTS THE AVERAGE RMS DIFFERENCE BETWEEN THE INDIVIDUAL 100 SIMULATED ANNEALING STRUCTURES AND THE MEAN COORDINATE POSITIONS FOR THE STRUCTURE OF THE PREVIOUSLY DETERMINED UNPHOSPHORYLATED STATE (PDB ACCESSION CODE 1VKR). EXPERIMENTAL RESTRAINTS INVOLVING THE PHOSPHORYLATED ACTIVE SITE RESIDUES 383-394: 83 NOE-DERIVED INTERPROTON DISTANCE RESTRAINTS (8 INTRARESIDUE, 17 SEQUENTIAL, 20 MEDIUM RANGE AND 38 LONG-RANGE INTERRESIDUE) 21 TORSION ANGLES (10 PHI, 9 PSI AND TWO CHI1) 11 N-H, 11 N-C' and 11 HN-C' RDCS IN PHAGE PF1 11 N-H, 6 N-C' AND 6 HN-C' RDCS IN NEUTRAL ANISOTROPIC GEL 10 N-H RDCS IN A POSITIVELY CHARGED ANISOTROPIC GEL 12 RESTRAINTS FOR 6 BACKBONE H-BONDS INVOLVING ONE ACTIVE SITE RESIDUE 2 RESTRAINTS FOR A PHOSPHORYL-NH(SER391) H-BOND DEMONSTRATED BY OBSERVATION OF A 3JNP COUPLING. THE TOTAL NUMBER OF RDCS MEASURED FOR THE WHOLE PROTEIN WAS: 192 IN PHAGE PF1, 139 IN NEUTRAL GEL, AND 55 IN POSITIVE GEL. EXCLUDING A FEW OUTLIERS INVOLVING ONLY RESIDUES 386-391 WITHIN THE ACTIVE SITE, THE REMAINING RDCS FIT THE STRUCTURE OF THE UNPHOSPHORYLATED STATE (COORDINATES 1VKR) EXTREMELY WELL INDICATING THAT THE ONLY BACKBONE CONFORMATIONAL CHANGES THAT OCCUR UPON PHOSPHORYLATION ARE LOCALIZED SPECIFICALLY TO THE ACTIVE SITE (RESIDUES 383-393). THEREFORE ONLY THE COORDINATES OF THE ACTIVE SITE WERE REFINED WITH THE COORDINATES OF THE REMAINDER OF THE PROTEIN FIXED TO THEIR POSITIONS IN 1VKR.
NMR ensemble
Conformer selection criteria: REGULARIZED MEAN STRUCTURE / Conformers calculated total number: 150 / Conformers submitted total number: 1
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