HEADER ANTIBIOTIC 06-JUN-96 1MAG TITLE GRAMICIDIN A IN HYDRATED DMPC BILAYERS, SOLID STATE NMR COMPND MOL_ID: 1; COMPND 2 MOLECULE: GRAMICIDIN A; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: VALYL GRAMICIDIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BREVIBACILLUS BREVIS; SOURCE 3 ORGANISM_TAXID: 1393 KEYWDS GRAMICIDIN, ANTIFUNGAL, ANTIBACTERIAL, ANTIBIOTIC, MEMBRANE ION KEYWDS 2 CHANNEL, LINEAR GRAMICIDIN, ORIENTED BILAYERS EXPDTA SOLID-STATE NMR AUTHOR R.R.KETCHEM,B.ROUX,T.A.CROSS REVDAT 8 16-OCT-24 1MAG 1 REMARK REVDAT 7 15-NOV-23 1MAG 1 LINK ATOM REVDAT 6 14-MAR-18 1MAG 1 REMARK REVDAT 5 20-DEC-17 1MAG 1 JRNL REVDAT 4 27-JUL-11 1MAG 1 ATOM HETATM REMARK SEQRES REVDAT 3 13-JUL-11 1MAG 1 VERSN REVDAT 2 24-FEB-09 1MAG 1 VERSN REVDAT 1 11-JAN-97 1MAG 0 JRNL AUTH R.R.KETCHEM,K.C.LEE,S.HUO,T.A.CROSS JRNL TITL MACROMOLECULAR STRUCTURAL ELUCIDATION WITH SOLID-STATE JRNL TITL 2 NMR-DERIVED ORIENTATIONAL CONSTRAINTS. JRNL REF J.BIOMOL.NMR V. 8 1 1996 JRNL REFN ISSN 0925-2738 JRNL PMID 8810522 JRNL DOI 10.1007/BF00198135 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH R.R.KETCHEM,B.ROUX,T.A.CROSS REMARK 1 TITL COMPUTATIONAL REFINEMENT THROUGH SOLID STATE NMR AND ENERGY REMARK 1 TITL 2 CONSTRAINTS OF A MEMBRANE BOUND POLYPEPTIDE REMARK 1 EDIT K.M.MERZ JUNIOR, B.ROUX REMARK 1 REF BIOLOGICAL MEMBRANES: A 299 1996 REMARK 1 REF 2 MOLECULAR PERSPECTIVE FROM REMARK 1 REF 3 COMPUTATION AND EXPERIMENT REMARK 1 PUBL BOSTON : BIRKHAUSER REMARK 1 REFN ISSN 0-8176-3827-X REMARK 1 REFERENCE 2 REMARK 1 AUTH K.C.LEE,S.HUO,T.A.CROSS REMARK 1 TITL LIPID-PEPTIDE INTERFACE: VALINE CONFORMATION AND DYNAMICS IN REMARK 1 TITL 2 THE GRAMICIDIN CHANNEL REMARK 1 REF BIOCHEMISTRY V. 34 857 1995 REMARK 1 REFN ISSN 0006-2960 REMARK 1 PMID 7530046 REMARK 1 DOI 10.1021/BI00003A020 REMARK 1 REFERENCE 3 REMARK 1 AUTH W.HU,N.D.LAZO,T.A.CROSS REMARK 1 TITL TRYPTOPHAN DYNAMICS AND STRUCTURAL REFINEMENT IN A LIPID REMARK 1 TITL 2 BILAYER ENVIRONMENT: SOLID STATE NMR OF THE GRAMICIDIN REMARK 1 TITL 3 CHANNEL REMARK 1 REF BIOCHEMISTRY V. 34 14138 1995 REMARK 1 REFN ISSN 0006-2960 REMARK 1 PMID 7578011 REMARK 1 DOI 10.1021/BI00043A019 REMARK 1 REFERENCE 4 REMARK 1 AUTH R.R.KETCHEM,W.HU,T.A.CROSS REMARK 1 TITL HIGH-RESOLUTION CONFORMATION OF GRAMICIDIN A IN A LIPID REMARK 1 TITL 2 BILAYER BY SOLID-STATE NMR REMARK 1 REF SCIENCE V. 261 1457 1993 REMARK 1 REFN ISSN 0036-8075 REMARK 1 PMID 7690158 REMARK 1 DOI 10.1126/SCIENCE.7690158 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TORC REMARK 3 AUTHORS : KETCHEM,ROUX,CROSS REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: CHARMM23 STRUCTURE REFINED WITH TORC REMARK 3 (TOTAL REFINEMENT OF CONSTRAINTS), DEVELOPED IN AUTHORS' LAB. REMARK 3 TORC RUNS AS A MODULE WITHIN CHARMM AND UTILIZES A SIMULATED REMARK 3 ANNEALING PROTOCOL TO REFINE THE STRUCTURE AGAINST BOTH THE REMARK 3 SOLID STATE NMR DATA (INCLUDING SOLID STATE NMR DERIVED REMARK 3 ORIENTATIONAL CONSTRAINTS) AND THE CHARMM ENERGY. REMARK 4 REMARK 4 1MAG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000174899. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : SOLID STATE; CROSS POLARIZED REMARK 210 SPECTROMETER FIELD STRENGTH : 400 MHZ REMARK 210 SPECTROMETER MODEL : CMX REMARK 210 SPECTROMETER MANUFACTURER : CHEMAGNETICS REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TORC REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: NULL REMARK 217 REMARK 217 SOLID STATE NMR STUDY REMARK 217 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLID REMARK 217 STATE NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 217 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 217 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 GRAMICIDIN IS A HETEROGENEOUS MIXTURE OF SEVERAL COMPOUNDS REMARK 400 INCLUDING GRAMICIDIN A, B AND C WHICH ARE OBTAINED FROM REMARK 400 BACILLUS BREVIS AND CALLED COLLECTIVELY GRAMICIDIN D REMARK 400 HERE, GRAMICIDIN A IS REPRESENTED BY THE SEQUENCE (SEQRES) REMARK 400 REMARK 400 THE GRAMICIDIN A IS POLYPEPTIDE, A MEMBER OF ANTIBIOTIC CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: GRAMICIDIN A REMARK 400 CHAIN: A, B REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 DESCRIPTION: GRAMICIDIN A IS A HEXADECAMERIC HELICAL PEPTIDE WITH REMARK 400 ALTERNATING D,L CHARACTERISTICS. THE N-TERM IS REMARK 400 FORMYLATED (RESIDUE 0). THE C-TERM IS CAPPED WITH REMARK 400 ETHANOLAMINE (RESIDUE 16). 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 DLE A 4 CB - CG - CD2 ANGL. DEV. = 17.7 DEGREES REMARK 500 DLE A 10 CB - CG - CD2 ANGL. DEV. = 10.6 DEGREES REMARK 500 DLE A 12 CB - CG - CD1 ANGL. DEV. = 14.2 DEGREES REMARK 500 DLE A 14 N - CA - CB ANGL. DEV. = -13.0 DEGREES REMARK 500 DLE A 14 CB - CG - CD1 ANGL. DEV. = 11.9 DEGREES REMARK 500 DLE B 4 CB - CG - CD2 ANGL. DEV. = 17.7 DEGREES REMARK 500 DLE B 10 CB - CG - CD2 ANGL. DEV. = 10.6 DEGREES REMARK 500 DLE B 12 CB - CG - CD1 ANGL. DEV. = 14.2 DEGREES REMARK 500 DLE B 14 N - CA - CB ANGL. DEV. = -13.0 DEGREES REMARK 500 DLE B 14 CB - CG - CD1 ANGL. DEV. = 11.9 DEGREES 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 CHAIN A OF GRAMICIDIN A REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN B OF GRAMICIDIN A REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1TK2 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF GRAMICIDIN S COMPLEXED WITH ALKALINE REMARK 900 PROTEINASE SAVINASE REMARK 900 RELATED ID: 2XDC RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF GRAMICIDIN A FROM CRYSTALS GROWN IN A LIPID REMARK 900 CUBIC PHASE. REMARK 900 RELATED ID: 1AV2 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF GRAMICIDIN A COMPLEXED WITH CESIUM CHLORIDE REMARK 900 RELATED ID: 1BDW RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF GRAMICIDIN A FROM BACILLUS BREVIS REMARK 900 RELATED ID: 1C4D RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF GRAMICIDIN A COMPLEXED WITH CESIUM CHLORIDE REMARK 900 RELATED ID: 1GMK RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF GRAMICIDIN A COMPLRXED WITH POTASSIUM REMARK 900 THIOCYANATE REMARK 900 RELATED ID: 1GRM RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE GRAMICIDIN A REMARK 900 RELATED ID: 1JNO RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF GRAMICIDIN A IN SODIUM DODECYL SULFATE REMARK 900 MICELLES REMARK 900 RELATED ID: 1KQE RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF A LINKED SHORTENED GRAMICIDIN A IN BENZENE/ REMARK 900 ACETONE 10:1 REMARK 900 RELATED ID: 1MIC RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF GRAMICIDIN A IN METHANOL IN THE PRESENCE OF REMARK 900 CACL REMARK 900 RELATED ID: 1NG8 RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF GRAMICIDIN A (W15G) IN SODIUM DODECYL SULFATE REMARK 900 MICELLES REMARK 900 RELATED ID: 1NRM RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF GRAMICIDIN A IN DODECYL PHOSPHOCHOLINE REMARK 900 MICELLES REMARK 900 RELATED ID: 1NRU RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF GRAMICIDIN A IN DODECYL PHOSPHOCHOLINE REMARK 900 MICELLES IN THE PRESENCE OF EXCESS NA+ REMARK 900 RELATED ID: 1NT5 RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF GRAMICIDIN A (V1F) IN SODIUM DODECYL SULFATE REMARK 900 MICELLES REMARK 900 RELATED ID: 1JO3 RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF GRAMICIDIN B IN SODIUM DODECYL SULFATE REMARK 900 MICELLES REMARK 900 RELATED ID: 1JO4 RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF GRAMICIDIN C IN SODIUM DODECYL SULFATE REMARK 900 MICELLES REMARK 900 RELATED ID: 1NT6 RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF F1-GRAMICIDIN C IN SODIUM DODECYL SULFATE REMARK 900 MICELLES REMARK 900 RELATED ID: 1TKQ RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF A LINKED UNSYMMETRIC GRAMICIDIN A IN A REMARK 900 MEMBRANE-ISOELECTRICAL SOLVENTS MIXTURE, IN THE PRESENCE OF CSCL REMARK 900 RELATED ID: 1W5U RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF GRAMICIDIN D IN ETHANOL REMARK 900 RELATED ID: 2IZQ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF GRAMICIDIN D COMPLEX WITH KI IN METHANOL REMARK 900 RELATED ID: 3L8L RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF GRAMICIDIN D COMPLEX WITH NAI REMARK 900 RELATED ID: 1AL4 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF GRAMICIDIN D IN N-PROPANOL REMARK 900 RELATED ID: 1ALX RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF GRAMICIDIN D IN METHANOL REMARK 900 RELATED ID: 1ALZ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF GRAMICIDIN D IN ETHANOL DBREF 1MAG A 1 16 NOR NOR00243 NOR00243 1 16 DBREF 1MAG B 1 16 NOR NOR00243 NOR00243 1 16 SEQRES 1 A 16 FVA GLY ALA DLE ALA DVA VAL DVA TRP DLE TRP DLE TRP SEQRES 2 A 16 DLE TRP ETA SEQRES 1 B 16 FVA GLY ALA DLE ALA DVA VAL DVA TRP DLE TRP DLE TRP SEQRES 2 B 16 DLE TRP ETA HET FVA A 1 19 HET DLE A 4 19 HET DVA A 6 16 HET DVA A 8 16 HET DLE A 10 19 HET DLE A 12 19 HET DLE A 14 19 HET ETA A 16 10 HET FVA B 1 19 HET DLE B 4 19 HET DVA B 6 16 HET DVA B 8 16 HET DLE B 10 19 HET DLE B 12 19 HET DLE B 14 19 HET ETA B 16 10 HETNAM FVA N-FORMYL-L-VALINE HETNAM DLE D-LEUCINE HETNAM DVA D-VALINE HETNAM ETA ETHANOLAMINE FORMUL 1 FVA 2(C6 H11 N O3) FORMUL 1 DLE 8(C6 H13 N O2) FORMUL 1 DVA 4(C5 H11 N O2) FORMUL 1 ETA 2(C2 H7 N O) SHEET 1 AA 2 GLY A 2 TRP A 15 0 SHEET 2 AA 2 GLY B 2 TRP B 15 -1 O ALA B 3 N ALA A 3 LINK C FVA A 1 N GLY A 2 1555 1555 1.34 LINK C ALA A 3 N DLE A 4 1555 1555 1.34 LINK C DLE A 4 N ALA A 5 1555 1555 1.37 LINK C ALA A 5 N DVA A 6 1555 1555 1.34 LINK C DVA A 6 N VAL A 7 1555 1555 1.35 LINK C VAL A 7 N DVA A 8 1555 1555 1.35 LINK C DVA A 8 N TRP A 9 1555 1555 1.35 LINK C TRP A 9 N DLE A 10 1555 1555 1.34 LINK C DLE A 10 N TRP A 11 1555 1555 1.34 LINK C TRP A 11 N DLE A 12 1555 1555 1.33 LINK C DLE A 12 N TRP A 13 1555 1555 1.34 LINK C TRP A 13 N DLE A 14 1555 1555 1.34 LINK C DLE A 14 N TRP A 15 1555 1555 1.35 LINK C TRP A 15 N ETA A 16 1555 1555 1.35 LINK C FVA B 1 N GLY B 2 1555 1555 1.34 LINK C ALA B 3 N DLE B 4 1555 1555 1.34 LINK C DLE B 4 N ALA B 5 1555 1555 1.37 LINK C ALA B 5 N DVA B 6 1555 1555 1.34 LINK C DVA B 6 N VAL B 7 1555 1555 1.35 LINK C VAL B 7 N DVA B 8 1555 1555 1.35 LINK C DVA B 8 N TRP B 9 1555 1555 1.35 LINK C TRP B 9 N DLE B 10 1555 1555 1.34 LINK C DLE B 10 N TRP B 11 1555 1555 1.34 LINK C TRP B 11 N DLE B 12 1555 1555 1.33 LINK C DLE B 12 N TRP B 13 1555 1555 1.34 LINK C TRP B 13 N DLE B 14 1555 1555 1.34 LINK C DLE B 14 N TRP B 15 1555 1555 1.35 LINK C TRP B 15 N ETA B 16 1555 1555 1.35 SITE 1 AC1 3 GLY B 2 ALA B 3 ALA B 5 SITE 1 AC2 3 GLY A 2 ALA A 3 ALA A 5 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 HETATM 1 C FVA A 1 -0.920 -3.596 -2.797 1.00 0.00 C HETATM 2 N FVA A 1 -3.043 -2.601 -3.416 1.00 0.00 N HETATM 3 O FVA A 1 -0.385 -3.961 -3.851 1.00 0.00 O HETATM 4 CA FVA A 1 -2.415 -3.640 -2.601 1.00 0.00 C HETATM 5 CB FVA A 1 -2.919 -5.045 -2.884 1.00 0.00 C HETATM 6 CG1 FVA A 1 -2.163 -6.141 -2.056 1.00 0.00 C HETATM 7 CG2 FVA A 1 -4.427 -5.132 -2.644 1.00 0.00 C HETATM 8 H FVA A 1 -2.760 -2.649 -4.381 1.00 0.00 H HETATM 9 HA FVA A 1 -2.651 -3.401 -1.570 1.00 0.00 H HETATM 10 HB FVA A 1 -2.542 -5.494 -3.836 1.00 0.00 H HETATM 11 HG11 FVA A 1 -2.280 -5.946 -0.974 1.00 0.00 H HETATM 12 HG12 FVA A 1 -2.578 -7.146 -2.278 1.00 0.00 H HETATM 13 HG13 FVA A 1 -1.080 -6.174 -2.292 1.00 0.00 H HETATM 14 O1 FVA A 1 -3.774 -1.363 -1.586 1.00 0.00 O HETATM 15 HG21 FVA A 1 -4.671 -4.794 -1.613 1.00 0.00 H HETATM 16 CN FVA A 1 -3.690 -1.575 -2.801 1.00 0.00 C HETATM 17 HG22 FVA A 1 -4.985 -4.505 -3.373 1.00 0.00 H HETATM 18 HG23 FVA A 1 -4.766 -6.182 -2.771 1.00 0.00 H HETATM 19 HN FVA A 1 -4.305 -1.047 -3.545 1.00 0.00 H