HEADER ANTIBIOTIC 28-JAN-03 1NT6 TITLE F1-GRAMICIDIN C IN SODIUM DODECYL SULFATE MICELLES (NMR) COMPND MOL_ID: 1; COMPND 2 MOLECULE: GRAMICIDIN C; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: BREVIBACILLUS BREVIS; SOURCE 4 ORGANISM_TAXID: 1393 KEYWDS GRAMICIDIN, ANTIFUNGAL, ANTIBACTERIAL, SDS MICELLES, MEMBRANE ION KEYWDS 2 CHANNEL, LINEAR GRAMICIDIN, ANTIBIOTIC EXPDTA SOLUTION NMR MDLTYP MINIMIZED AVERAGE AUTHOR L.E.TOWNSLEY,T.G.FLETCHER,J.F.HINTON REVDAT 5 15-NOV-23 1NT6 1 SEQADV LINK ATOM REVDAT 4 27-JUL-11 1NT6 1 ATOM HETATM REMARK SEQRES REVDAT 3 13-JUL-11 1NT6 1 VERSN REVDAT 2 24-FEB-09 1NT6 1 VERSN REVDAT 1 11-FEB-03 1NT6 0 JRNL AUTH S.S.SHAM,S.SHOBANA,L.E.TOWNSLEY,J.B.JORDAN,J.Q.FERNANDEZ, JRNL AUTH 2 O.S.ANDERSEN,D.V.GREATHOUSE,J.F.HINTON JRNL TITL THE STRUCTURE, CATION BINDING, TRANSPORT, AND CONDUCTANCE OF JRNL TITL 2 GLY15-GRAMICIDIN A INCORPORATED INTO SDS MICELLES AND PC/PG JRNL TITL 3 VESICLES. JRNL REF BIOCHEMISTRY V. 42 1401 2003 JRNL REFN ISSN 0006-2960 JRNL PMID 12578352 JRNL DOI 10.1021/BI0204286 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DISCOVER 97.2 REMARK 3 AUTHORS : BIOSYM/MSI REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE WAS MODELED USING 602 REMARK 3 DISTANCE CONSTRAINTS AND 13 HYDROGEN BOND CONSTRAINTS PER REMARK 3 MONOMER, INCLUDING CONSTRAINTS BETWEEN THE MONOMERS. THE C2 REMARK 3 SYMMETRY CONSTRAINT DOUBLES THIS NUMBER OF CONSTRAINTS FOR THE REMARK 3 DIMER. 100 STRUCTURES WERE GENERATED USING DSPACE, OF WHICH THE REMARK 3 10 WITH THE FEWEST VIOLATIONS FROM THE DISTANCE CONSTRAINTS WERE REMARK 3 CHOSEN FOR THE AVERAGE STRUCTURE. THIS AVERAGE STRUCTURE WAS REMARK 3 FURTHER REFINED BY CONSTRAINED MINIMIZATION WITH DISCOVER USING REMARK 3 THE ALL-ATOM AMBER FORCE FIELD AND A DIELECTRIC CONSTANT OF 2.0 REMARK 3 TO EMULATE THAT OF THE MICELLE INTERIOR. REMARK 4 REMARK 4 1NT6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-JAN-03. REMARK 100 THE DEPOSITION ID IS D_1000018178. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 328 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 5MM F1-GRAMICIDIN C, 250MM REMARK 210 DEUTERATED SODIUM DODECYL REMARK 210 SULFATE, 80% 100MM PHOSPHATE REMARK 210 BUFFER PH 6.5, 10% D2O, 10% REMARK 210 DEUTERATED TFE REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : VXRS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMR 3.2, FELIX 95.0, DSPACE 4.0 REMARK 210 METHOD USED : DISTANCE GEOMETRY, SIMULATED REMARK 210 ANNEALING, RELAXATION MATRIX REMARK 210 CALCULATION, MINIMIZATION 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: A 40MSEC MIXING TIME WAS USED IN THE NOESY EXPERIMENT FROM REMARK 210 WHICH DISTANCE CONSTRAINTS WERE OBTAINED. 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 860 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 2730 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 KCAL/MOL 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 C IS REPRESENTED BY THE SEQUENCE (SEQRES) REMARK 400 REMARK 400 THE GRAMICIDIN C IS POLYPEPTIDE, A MEMBER OF ANTIBIOTIC CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: GRAMICIDIN C 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: 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 DLE A 4 -87.34 157.94 REMARK 500 DLE B 4 -87.34 157.86 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 C REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN B OF GRAMICIDIN C 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: 1MAG RELATED DB: PDB REMARK 900 SOLID STATE NMR STRUCTURE OF GRAMICIDIN A IN HYDRATED DMPC BILAYERS, 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: 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 1NT6 A 1 16 NOR NOR00245 NOR00245 1 16 DBREF 1NT6 B 1 16 NOR NOR00245 NOR00245 1 16 SEQADV 1NT6 QPH A 1 NOR NOR00245 FVA 1 ENGINEERED MUTATION SEQADV 1NT6 QPH B 1 NOR NOR00245 FVA 1 ENGINEERED MUTATION SEQRES 1 A 16 QPH GLY ALA DLE ALA DVA VAL DVA TRP DLE TYR DLE TRP SEQRES 2 A 16 DLE TRP ETA SEQRES 1 B 16 QPH GLY ALA DLE ALA DVA VAL DVA TRP DLE TYR DLE TRP SEQRES 2 B 16 DLE TRP ETA HET QPH A 1 23 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 QPH B 1 23 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 QPH N-FORMYL-L-PHENYLALANINE HETNAM DLE D-LEUCINE HETNAM DVA D-VALINE HETNAM ETA ETHANOLAMINE FORMUL 1 QPH 2(C10 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 QPH 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 1.34 LINK C ALA A 5 N DVA A 6 1555 1555 1.34 LINK C DVA A 6 N VAL A 7 1555 1555 1.34 LINK C VAL A 7 N DVA A 8 1555 1555 1.34 LINK C DVA A 8 N TRP A 9 1555 1555 1.34 LINK C TRP A 9 N DLE A 10 1555 1555 1.34 LINK C DLE A 10 N TYR A 11 1555 1555 1.34 LINK C TYR A 11 N DLE A 12 1555 1555 1.34 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 1.34 LINK C TRP A 15 N ETA A 16 1555 1555 1.34 LINK C QPH 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 1.34 LINK C ALA B 5 N DVA B 6 1555 1555 1.34 LINK C DVA B 6 N VAL B 7 1555 1555 1.34 LINK C VAL B 7 N DVA B 8 1555 1555 1.34 LINK C DVA B 8 N TRP B 9 1555 1555 1.34 LINK C TRP B 9 N DLE B 10 1555 1555 1.34 LINK C DLE B 10 N TYR B 11 1555 1555 1.34 LINK C TYR B 11 N DLE B 12 1555 1555 1.34 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 1.34 LINK C TRP B 15 N ETA B 16 1555 1555 1.34 SITE 1 AC1 4 GLY B 2 ALA B 3 DLE B 4 ALA B 5 SITE 1 AC2 4 GLY A 2 ALA A 3 DLE A 4 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 0.000000 1.000000 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 QPH A 1 0.001 1.032 2.444 1.00 0.00 C HETATM 2 N QPH A 1 -2.398 0.340 2.210 1.00 0.00 N HETATM 3 O QPH A 1 0.465 0.037 1.886 1.00 0.00 O HETATM 4 CA QPH A 1 -1.410 0.995 3.065 1.00 0.00 C HETATM 5 CB QPH A 1 -1.377 0.257 4.413 1.00 0.00 C HETATM 6 CG QPH A 1 -0.793 1.060 5.554 1.00 0.00 C HETATM 7 CZ QPH A 1 0.309 2.656 7.602 1.00 0.00 C HETATM 8 CD1 QPH A 1 0.605 1.115 5.729 1.00 0.00 C HETATM 9 CD2 QPH A 1 -1.644 1.786 6.414 1.00 0.00 C HETATM 10 CE1 QPH A 1 1.158 1.916 6.751 1.00 0.00 C HETATM 11 CE2 QPH A 1 -1.092 2.588 7.437 1.00 0.00 C HETATM 12 H QPH A 1 -2.087 -0.458 1.669 1.00 0.00 H HETATM 13 HA QPH A 1 -1.743 2.016 3.244 1.00 0.00 H HETATM 14 HZ QPH A 1 0.732 3.274 8.382 1.00 0.00 H HETATM 15 HB2 QPH A 1 -2.380 -0.068 4.695 1.00 0.00 H HETATM 16 HB3 QPH A 1 -0.772 -0.637 4.290 1.00 0.00 H HETATM 17 HD1 QPH A 1 1.239 0.545 5.066 1.00 0.00 H HETATM 18 O1 QPH A 1 -4.159 1.569 2.884 1.00 0.00 O HETATM 19 HD2 QPH A 1 -2.717 1.730 6.276 1.00 0.00 H HETATM 20 CN QPH A 1 -3.706 0.610 2.262 1.00 0.00 C HETATM 21 HE1 QPH A 1 2.230 1.962 6.880 1.00 0.00 H HETATM 22 HE2 QPH A 1 -1.742 3.153 8.090 1.00 0.00 H HETATM 23 HNA QPH A 1 -4.398 -0.044 1.744 1.00 0.00 H