HEADER ANTIBIOTIC 31-AUG-04 1VM3 TITLE SOLUTION STRUCTURE OF A MEMBRANE-TARGETING PEPTIDE DESIGNED BASED ON TITLE 2 THE N-TERMINAL SEQUENCE OF E. COLI ENZYME IIA (GLUCOSE) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDE A3; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 OTHER_DETAILS: THE PEPTIDE WAS SYNTHESIZED USING THE SOLID-PHASE SOURCE 6 METHOD AND PURIFIED BY HPLC. KEYWDS AMPHIPATHIC HELIX, ANTIMICROBIAL PEPTIDE, BACTERIAL MEMBRANE ANCHOR, KEYWDS 2 MEMBRANE BINDING, ANTIBIOTIC EXPDTA SOLUTION NMR NUMMDL 5 AUTHOR G.WANG,X.LI REVDAT 6 13-NOV-24 1VM3 1 REMARK REVDAT 5 27-DEC-23 1VM3 1 REMARK REVDAT 4 24-JUN-20 1VM3 1 SOURCE REMARK DBREF LINK REVDAT 3 17-FEB-09 1VM3 1 AUTHOR VERSN REVDAT 2 01-MAR-05 1VM3 1 JRNL REVDAT 1 07-DEC-04 1VM3 0 JRNL AUTH G.WANG,Y.LI,X.LI JRNL TITL CORRELATION OF THREE-DIMENSIONAL STRUCTURES WITH THE JRNL TITL 2 ANTIBACTERIAL ACTIVITY OF A GROUP OF PEPTIDES DESIGNED BASED JRNL TITL 3 ON A NONTOXIC BACTERIAL MEMBRANE ANCHOR. JRNL REF J.BIOL.CHEM. V. 280 5803 2005 JRNL REFN ISSN 0021-9258 JRNL PMID 15572363 JRNL DOI 10.1074/JBC.M410116200 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE/NMRDRAW 2.1, XPLOR-NIH 1.06 REMARK 3 AUTHORS : DELAGLIO, F. (NMRPIPE/NMRDRAW), SCHWIETERS, C.D., REMARK 3 KUSZEWSKI, J., TJANDRA, N, CLORE, G.M. (XPLOR-NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON 104 REMARK 3 DISTANCES DERIVED FROM THE NOESY SPECTRA, 20 BACKBONE DIHEDRAL REMARK 3 ANGLES DERIVED FROM A SET OF CHEMICAL SHIFTS USING THE NMR REMARK 3 PROGRAM TALOS, AND 5 CHI1 ANGLE RESTRAINTS. REMARK 4 REMARK 4 1VM3 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-SEP-04. REMARK 100 THE DEPOSITION ID IS D_1000001999. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 5.4 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 2MM PEPTIDE, 80MM SODIUM REMARK 210 DODECYLSULFATE, 90% H2O AND 10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; TOCSY; DQF-COSY; REMARK 210 (1H,15N)HSQC; (1H,13C)HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : PIPP 1.0, MOLMOL 2K.1 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 5 REMARK 210 CONFORMERS, SELECTION CRITERIA : NO NOE VIOLATIONS GREATER THAN REMARK 210 0.50 A, RMS DIFFERENCE FOR BOND REMARK 210 DEVIATIONS FROM IDEALITY LESS REMARK 210 THAN 0.01 A, RMS DIFFERENCE FOR REMARK 210 ANGLE DEVIATIONS FROM IDEALITY REMARK 210 LESS THAN 5 DEGREES, STRUCTURES REMARK 210 WITH THE LOWEREST ENERGIES IN REMARK 210 THE ENSEMBLE. REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D REMARK 210 HOMONUCLEAR NMR TECHNIQUES, PLUS THE USE OF BACKBONE ANGLE REMARK 210 RESTRAINTS DERIVED FROM A SET OF HETERONUCLEAR CHEMICAL SHIFTS REMARK 210 MEASURED ON THE NATURAL ABUNDANCE PEPTIDE BOUND TO MICELLES. REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 1 ASP A 12 -87.59 -87.57 REMARK 500 2 LEU A 2 -19.19 -44.90 REMARK 500 2 ASP A 12 -79.01 -89.97 REMARK 500 3 ASP A 12 -74.50 -89.84 REMARK 500 4 ASP A 12 -84.30 -90.71 REMARK 500 5 ASP A 12 -83.53 -90.94 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NH2 A 14 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1O53 RELATED DB: PDB REMARK 900 NMR STRUCTURE OF THE MEMBRANE ANCHOR REMARK 900 RELATED ID: 1VM2 RELATED DB: PDB REMARK 900 RELATED ID: 1VM4 RELATED DB: PDB REMARK 900 RELATED ID: 1VM5 RELATED DB: PDB DBREF 1VM3 A 1 14 PDB 1VM3 1VM3 1 14 SEQRES 1 A 14 GLY LEU PHE ASP ILE VAL LYS SER LEU VAL SER ASP PHE SEQRES 2 A 14 NH2 HET NH2 A 14 3 HETNAM NH2 AMINO GROUP FORMUL 1 NH2 H2 N HELIX 1 1 LEU A 2 VAL A 10 1 9 LINK C PHE A 13 N NH2 A 14 1555 1555 1.31 SITE 1 AC1 3 VAL A 10 ASP A 12 PHE A 13 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1