HEADER ANTIMICROBIAL PROTEIN 20-SEP-17 6B34 TITLE NMR ENSEMBLE OF TYROCIDINE A ANALOGUE AC3.27 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYROCIDINE A ANALOGUE D-PHE-BE2-PHE-D-PHE-ASN-GLN-TYR-VAL- COMPND 3 ORN-LEU; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: BREVIBACILLUS BREVIS; SOURCE 4 ORGANISM_TAXID: 1393; SOURCE 5 OTHER_DETAILS: SYNTHETIC ANALOGUE OF TYROCIDINE A. SEQUENCE IS SOURCE 6 ALTERED AT 2 POSITIONS RELATIVE TO NATURAL PRODUCT. KEYWDS TYROCIDINE A ANTIMICROBIAL PEPTIDE AMP CYCLIC PEPTIDE 2-AMINOBENZOIC KEYWDS 2 ACID 2-ABZ ANTHRANILIC ACID, ANTIMICROBIAL PROTEIN EXPDTA SOLUTION NMR NUMMDL 9 AUTHOR A.J.CAMERON,P.J.B.EWDARDS,E.HARJES,V.SAROJINI REVDAT 5 15-NOV-23 6B34 1 LINK ATOM REVDAT 4 14-JUN-23 6B34 1 REMARK REVDAT 3 12-AUG-20 6B34 1 REMARK LINK ATOM REVDAT 2 27-DEC-17 6B34 1 JRNL REVDAT 1 06-DEC-17 6B34 0 JRNL AUTH A.J.CAMERON,P.J.B.EDWARDS,E.HARJES,V.SAROJINI JRNL TITL TYROCIDINE A ANALOGUES BEARING THE PLANAR D-PHE-2-ABZ TURN JRNL TITL 2 MOTIF: HOW CONFORMATION IMPACTS BIOACTIVITY. JRNL REF J. MED. CHEM. V. 60 9565 2017 JRNL REFN ISSN 1520-4804 JRNL PMID 29140694 JRNL DOI 10.1021/ACS.JMEDCHEM.7B00953 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : YASARA REMARK 3 AUTHORS : KRIEGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6B34 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-SEP-17. REMARK 100 THE DEPOSITION ID IS D_1000230147. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.7 MM NONE D-PHE-2-ABZ-PHE-D REMARK 210 -PHE-ASN-GLN-TYR-VAL-ORN-LEU, 50% REMARK 210 H20 / 50% MECN REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D DQF-COSY; 2D REMARK 210 1H-15N HSQC; 2D 1H-1H TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : YASARA, ANALYSIS 2.4.2 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 10 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 9 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE REMARK 210 COVALENT GEOMETRY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL 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 400 REMARK 400 COMPOUND REMARK 400 TYROCIDINE KILLS BACTERIA BY INTERACTING WITH THEIR CYTOPLASMIC REMARK 400 MEMBRANE AND CAUSING LEAKAGE OF THEIR INTRACELLULAR CONTENT. IT REMARK 400 ALSO AFFECTS INTRACELLULAR MEMBRANES SUCH AS THOSE OF MITOCHONDRIA REMARK 400 REMARK 400 THE TYROCIDINE A ANALOGUE (DPN)(BE2)F(DPN)NQYV(ORN)L IS CYCLIC REMARK 400 PEPTIDE, A MEMBER OF ANTIBIOTIC CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: TYROCIDINE A ANALOGUE (DPN)(BE2)F(DPN)NQYV(ORN)L REMARK 400 CHAIN: A REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 DESCRIPTION: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 1 BE2 A 2 CA - C - N ANGL. DEV. = 28.6 DEGREES REMARK 500 2 BE2 A 2 CA - C - N ANGL. DEV. = 28.0 DEGREES REMARK 500 3 BE2 A 2 CA - C - N ANGL. DEV. = 24.6 DEGREES REMARK 500 4 BE2 A 2 CA - C - N ANGL. DEV. = 27.3 DEGREES REMARK 500 5 BE2 A 2 CA - C - N ANGL. DEV. = 27.4 DEGREES REMARK 500 6 BE2 A 2 CA - C - N ANGL. DEV. = 26.2 DEGREES REMARK 500 7 BE2 A 2 CA - C - N ANGL. DEV. = 28.2 DEGREES REMARK 500 8 BE2 A 2 CA - C - N ANGL. DEV. = 24.6 DEGREES REMARK 500 9 BE2 A 2 CA - C - N ANGL. DEV. = 26.4 DEGREES 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 DPN A 4 -158.57 -84.94 REMARK 500 2 DPN A 4 -160.49 -85.00 REMARK 500 3 DPN A 4 -102.08 -81.07 REMARK 500 4 BE2 A 2 -164.53 -170.38 REMARK 500 4 DPN A 4 -160.02 -158.76 REMARK 500 5 DPN A 4 -155.42 -84.84 REMARK 500 6 DPN A 4 -155.86 -84.93 REMARK 500 7 DPN A 4 -157.77 -84.92 REMARK 500 8 DPN A 4 -103.78 -81.05 REMARK 500 9 DPN A 4 -133.81 -81.97 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 3 BE2 A 2 11.35 REMARK 500 8 BE2 A 2 10.91 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30346 RELATED DB: BMRB REMARK 900 NMR ENSEMBLE OF TYROCIDINE A ANALOGUE AC3.27 DBREF 6B34 A 1 10 PDB 6B34 6B34 1 10 SEQRES 1 A 10 DPN BE2 PHE DPN ASN GLN TYR VAL ORN LEU HET DPN A 1 20 HET BE2 A 2 14 HET DPN A 4 20 HET ORN A 9 19 HETNAM DPN D-PHENYLALANINE HETNAM BE2 2-AMINOBENZOIC ACID HETNAM ORN L-ORNITHINE FORMUL 1 DPN 2(C9 H11 N O2) FORMUL 1 BE2 C7 H7 N O2 FORMUL 1 ORN C5 H12 N2 O2 LINK C DPN A 1 N BE2 A 2 1555 1555 1.40 LINK N DPN A 1 C LEU A 10 1555 1555 1.33 LINK C BE2 A 2 N PHE A 3 1555 1555 1.39 LINK C PHE A 3 N DPN A 4 1555 1555 1.33 LINK C DPN A 4 N ASN A 5 1555 1555 1.32 LINK C VAL A 8 N ORN A 9 1555 1555 1.33 LINK C ORN A 9 N LEU A 10 1555 1555 1.33 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 HETATM 1 N DPN A 1 1.842 -5.130 -2.355 1.00 0.00 N HETATM 2 CA DPN A 1 3.203 -5.719 -2.334 1.00 0.00 C HETATM 3 C DPN A 1 4.089 -5.073 -3.409 1.00 0.00 C HETATM 4 O DPN A 1 4.550 -5.769 -4.305 1.00 0.00 O HETATM 5 CB DPN A 1 3.866 -5.816 -0.933 1.00 0.00 C HETATM 6 CG DPN A 1 5.285 -5.311 -0.885 1.00 0.00 C HETATM 7 CD1 DPN A 1 5.579 -4.077 -0.281 1.00 0.00 C HETATM 8 CD2 DPN A 1 6.338 -6.070 -1.434 1.00 0.00 C HETATM 9 CE1 DPN A 1 6.909 -3.589 -0.236 1.00 0.00 C HETATM 10 CE2 DPN A 1 7.672 -5.594 -1.394 1.00 0.00 C HETATM 11 CZ DPN A 1 7.955 -4.347 -0.798 1.00 0.00 C HETATM 12 H DPN A 1 1.173 -5.587 -2.956 1.00 0.00 H HETATM 13 HA DPN A 1 3.080 -6.752 -2.659 1.00 0.00 H HETATM 14 HB2 DPN A 1 3.276 -5.279 -0.200 1.00 0.00 H HETATM 15 HB3 DPN A 1 3.873 -6.866 -0.637 1.00 0.00 H HETATM 16 HD1 DPN A 1 4.782 -3.489 0.152 1.00 0.00 H HETATM 17 HD2 DPN A 1 6.127 -7.024 -1.901 1.00 0.00 H HETATM 18 HE1 DPN A 1 7.120 -2.633 0.223 1.00 0.00 H HETATM 19 HE2 DPN A 1 8.470 -6.180 -1.827 1.00 0.00 H HETATM 20 HZ DPN A 1 8.969 -3.975 -0.773 1.00 0.00 H HETATM 21 C BE2 A 2 5.077 -1.048 -2.287 1.00 0.00 C HETATM 22 O BE2 A 2 4.335 -1.691 -1.569 1.00 0.00 O HETATM 23 C1 BE2 A 2 5.453 -1.517 -3.692 1.00 0.00 C HETATM 24 CA BE2 A 2 5.054 -2.815 -4.158 1.00 0.00 C HETATM 25 C3 BE2 A 2 5.400 -3.203 -5.475 1.00 0.00 C HETATM 26 N BE2 A 2 4.302 -3.699 -3.297 1.00 0.00 N HETATM 27 C4 BE2 A 2 6.129 -2.351 -6.311 1.00 0.00 C HETATM 28 C5 BE2 A 2 6.525 -1.094 -5.860 1.00 0.00 C HETATM 29 C6 BE2 A 2 6.194 -0.672 -4.571 1.00 0.00 C HETATM 30 H3 BE2 A 2 5.102 -4.165 -5.867 1.00 0.00 H HETATM 31 H BE2 A 2 3.897 -3.253 -2.475 1.00 0.00 H HETATM 32 H4 BE2 A 2 6.383 -2.671 -7.317 1.00 0.00 H HETATM 33 H5 BE2 A 2 7.089 -0.438 -6.518 1.00 0.00 H HETATM 34 H6 BE2 A 2 6.513 0.319 -4.273 1.00 0.00 H