PDB Short entry for 1TKQ HEADER ANTIBIOTIC 09-JUN-04 1TKQ TITLE SOLUTION STRUCTURE OF A LINKED UNSYMMETRIC GRAMICIDIN IN A MEMBRANE- TITLE 2 ISOELECTRICAL SOLVENTS MIXTURE IN THE PRESENCE OF CSCL COMPND MOL_ID: 1; COMPND 2 MOLECULE: MINI-GRAMICIDIN A; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: GRAMICIDIN A; COMPND 7 CHAIN: B; COMPND 8 SYNONYM: VALYL GRAMICIDIN; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: BREVIBACILLUS BREVIS; SOURCE 4 ORGANISM_TAXID: 1393; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: BREVIBACILLUS BREVIS; SOURCE 8 ORGANISM_TAXID: 1393 KEYWDS GRAMICIDIN, ANTIFUNGAL, ANTIBACTERIAL, ANTIBIOTIC, MEMBRANE ION KEYWDS 2 CHANNEL, LINEAR GRAMICIDIN EXPDTA SOLUTION NMR MDLTYP MINIMIZED AVERAGE AUTHOR X.XIE,L.AL-MOMANI,D.BOCKELMANN,C.GRIESINGER,U.KOERT REVDAT 6 25-SEP-19 1TKQ 1 REMARK LINK ATOM REVDAT 5 27-JUL-11 1TKQ 1 ATOM HET HETATM LINK REVDAT 5 2 1 REMARK REVDAT 4 13-JUL-11 1TKQ 1 VERSN REVDAT 3 24-FEB-09 1TKQ 1 VERSN REVDAT 2 12-APR-05 1TKQ 1 JRNL REVDAT 1 13-JUL-04 1TKQ 0 JRNL AUTH X.XIE,L.AL-MOMANI,P.REISS,C.GRIESINGER,U.KOERT JRNL TITL AN ASYMMETRIC ION CHANNEL DERIVED FROM GRAMICIDIN A. JRNL TITL 2 SYNTHESIS, FUNCTION AND NMR STRUCTURE. JRNL REF FEBS J. V. 272 975 2005 JRNL REFN ISSN 1742-464X JRNL PMID 15691331 JRNL DOI 10.1111/J.1742-4658.2004.04531.X REMARK 1 REMARK 1 REFERENCE 1 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 1 REFERENCE 2 REMARK 1 AUTH Y.CHEN,A.TUCKER,B.A.WALLACE REMARK 1 TITL SOLUTION STRUCTURE OF A PARALLEL LEFT-HANDED DOUBLE-HELICAL REMARK 1 TITL 2 GRAMICIDIN-A DETERMINED BY 2D 1H NMR REMARK 1 REF J.MOL.BIOL. V. 264 757 1996 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 8980684 REMARK 1 DOI 10.1006/JMBI.1996.0675 REMARK 1 REFERENCE 3 REMARK 1 AUTH H.-D.ARNDT,D.BOCKELMANN,A.KNOLL,S.LAMBERTH,C.GRIESINGER, REMARK 1 AUTH 2 U.KOERT REMARK 1 TITL CATION CONTROL IN FUNCTIONAL HELICAL PROGRAMMING: STRUCTURES REMARK 1 TITL 2 OF A D,L-PEPTIDE ION CHANNEL REMARK 1 REF ANGEW.CHEM.INT.ED.ENGL. V. 41 4062 2002 REMARK 1 REFN ISSN 1433-7851 REMARK 1 PMID 12412082 REMARK 1 DOI 10.1002/1521-3773(20021104)41:21<4062::AID-ANIE4062>3.0.CO;2 REMARK 1 DOI 2 -U REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SYBYL/DYANA 6.8 REMARK 3 AUTHORS : GUENTERT REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON 160 NOE- REMARK 3 DERIVED DISTANCE CONSTRAINTS, 39 DIHEDRAL ANGLE RESTRAINTS, AND REMARK 3 40 DISTANCE RESTRAINTS FROM HYDROGEN BONDS REMARK 4 REMARK 4 1TKQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-JUN-04. REMARK 100 THE DEPOSITION ID IS D_1000022727. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : NULL REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : 3MM SATURATED WITH CSCL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : DQF-COSY; 2D NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SYBYL/DYANA 6.8 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : MINIMIZED AVERAGE STRUCTURE OF REMARK 210 11 STRUCTURES WITH THE LOWEST REMARK 210 TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: VARIABLE TEMPERATURE EXPERIMENTS WERE PERFORMED TO HAVE REMARK 210 THE TEMPERATURE DEPENDENCE OF NH CHEMICAL SHIFTS, THEREFORE REMARK 210 PROVIDE EVIDENCE FOR HYDROGEN BONDING. 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 760 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 2810 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 6.0 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, MODIFIDED GRAMICIDIN A IS REPRESENTED BY TWO SEQUENCES (SEQRES REMARK 400 AND ONE HET (SIN) REMARK 400 REMARK 400 THE MINI-GRAMICIDIN A - GRAMICIDIN A DIMER IS POLYPEPTIDE, A MEMBER REMARK 400 OF ANTIBIOTIC CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: MINI-GRAMICIDIN A - GRAMICIDIN A DIMER REMARK 400 CHAIN: A, B REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 COMPONENT_2: PEPTIDE LIKE POLYMER REMARK 400 COMPONENT_3: RESIDUE SIN REMARK 400 DESCRIPTION: THE N-TERMINI OF THE TWO PEPTIDES, EACH A TRUNCATED REMARK 400 GRAMICIDIN A, WERE LINKED BY A SUCCINIC ACID IN A REMARK 400 HEAD-TO-HEAD MANNER. 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 TRP A 15 CE2 - CD2 - CG ANGL. DEV. = -4.9 DEGREES REMARK 500 TRP B 9 CE2 - CD2 - CG ANGL. DEV. = -4.9 DEGREES REMARK 500 TRP B 11 CE2 - CD2 - CG ANGL. DEV. = -4.9 DEGREES REMARK 500 TRP B 13 CE2 - CD2 - CG ANGL. DEV. = -4.9 DEGREES REMARK 500 TRP B 15 CE2 - CD2 - CG ANGL. DEV. = -4.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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: 1NT6 RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF F1-GRAMICIDIN C IN SODIUM DODECYL SULFATE REMARK 900 MICELLES 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 REMARK 999 REMARK 999 SEQUENCE REMARK 999 BOTH OF THE C-TERMINI HAVE ETHANOLAMINE ATTACHED WITH REMARK 999 THE CAPPING GROUP T-BUTYLDIPHENYLSILYL, WHICH WAS APPLIED REMARK 999 TO ENHANCE THE SOLUBILITY AND STABILITY OF THE STRUCTURE REMARK 999 IN ORGANIC SOLVENTS. OWING TO AMBIGUITY IN RESONANCE REMARK 999 ASSIGNMENT OF THE TERMINI AND THEREFORE A LACK OF ENOUGH REMARK 999 NOE CONSTRAINTS, THE T-BUTYLDIPHENYLSILYL TERMINI WERE REMARK 999 OMITTED IN THE STRUCTURE CALCULATION. DBREF 1TKQ A 5 15 NOR NOR00243 NOR00243 5 15 DBREF 1TKQ B 1 15 NOR NOR00243 NOR00243 1 15 SEQRES 1 A 11 ALA DVA VAL DVA TRP DLE TRP DLE TRP DLE TRP SEQRES 1 B 15 VAL GLY ALA DLE ALA DVA VAL DVA TRP DLE TRP DLE TRP SEQRES 2 B 15 DLE TRP HET DVA A 6 15 HET DVA A 8 15 HET DLE A 10 19 HET DLE A 12 19 HET DLE A 14 19 HET DLE B 4 19 HET DVA B 6 15 HET DVA B 8 15 HET DLE B 10 19 HET DLE B 12 19 HET DLE B 14 19 HET SIN B 101 8 HETNAM DVA D-VALINE HETNAM DLE D-LEUCINE HETNAM SIN SUCCINIC ACID FORMUL 1 DVA 4(C5 H11 N O2) FORMUL 1 DLE 7(C6 H13 N O2) FORMUL 3 SIN C4 H6 O4 SHEET 1 AA 3 DLE A 12 TRP A 15 0 SHEET 2 AA 3 DVA A 6 TRP A 9 1 O DVA A 6 N TRP A 13 SHEET 3 AA 3 GLY B 2 TRP B 15 -1 O ALA B 3 N VAL A 7 LINK C ALA A 5 N DVA A 6 1555 1555 1.36 LINK C DVA A 6 N VAL A 7 1555 1555 1.35 LINK C VAL A 7 N DVA A 8 1555 1555 1.36 LINK C DVA A 8 N TRP A 9 1555 1555 1.36 LINK C TRP A 9 N DLE A 10 1555 1555 1.36 LINK C DLE A 10 N TRP A 11 1555 1555 1.36 LINK C TRP A 11 N DLE A 12 1555 1555 1.36 LINK C DLE A 12 N TRP A 13 1555 1555 1.36 LINK C TRP A 13 N DLE A 14 1555 1555 1.36 LINK C DLE A 14 N TRP A 15 1555 1555 1.35 LINK C ALA B 3 N DLE B 4 1555 1555 1.35 LINK C DLE B 4 N ALA B 5 1555 1555 1.35 LINK C ALA B 5 N DVA B 6 1555 1555 1.36 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 1.36 LINK C TRP B 9 N DLE B 10 1555 1555 1.35 LINK C DLE B 10 N TRP B 11 1555 1555 1.36 LINK C TRP B 11 N DLE B 12 1555 1555 1.35 LINK C DLE B 12 N TRP B 13 1555 1555 1.35 LINK C TRP B 13 N DLE B 14 1555 1555 1.35 LINK C DLE B 14 N TRP B 15 1555 1555 1.35 LINK C4 SIN B 101 N VAL B 1 1555 1555 1.35 LINK C1 SIN B 101 N ALA A 5 1555 1555 1.35 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