HEADER ANTIBIOTIC 07-OCT-08 2K9B TITLE STRUCTURE AND MEMBRANE INTERACTIONS OF THE ANTIBIOTIC PEPTIDE TITLE 2 DERMADISTINCTIN K BY MULTIDIMENSIONAL SOLUTION AND ORIENTED 15N AND TITLE 3 31P SOLID-STATE NMR SPECTROSCOPY COMPND MOL_ID: 1; COMPND 2 MOLECULE: DERMADISTINCTIN-K; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DD K; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THE PEPTIDE WAS PREPARED BY SOLID-PHASE SYNTHESIS SOURCE 4 USING FMOC CHEMISTRY KEYWDS AMPHIPATHIC ALPHA-HELIX, MEMBRANE PROTEIN STRUCTURE DETERMINATION, C- KEYWDS 2 TERMINAL CARBOXYAMIDATION, ANTIMICROBIAL PROTEIN, AMPHIBIAN DEFENSE KEYWDS 3 PEPTIDE, ANTIBIOTIC, ANTIMICROBIAL, SECRETED EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR C.M.MORAES,R.M.VERLY,J.M.RESENDE,C.AISENBREY,M.P.BEMQUERER,D.PILO- AUTHOR 2 VELOSO,A.VALENTE,F.C.L.ALMEIDA,B.BECHINGER REVDAT 2 16-MAR-22 2K9B 1 REMARK SEQADV LINK REVDAT 1 14-APR-09 2K9B 0 JRNL AUTH R.M.VERLY,C.M.DE MORAES,J.M.RESENDE,C.AISENBREY, JRNL AUTH 2 M.P.BEMQUERER,D.PILO-VELOSO,A.P.VALENTE,F.C.L.ALMEIDA, JRNL AUTH 3 B.BECHINGER JRNL TITL STRUCTURE AND MEMBRANE INTERACTIONS OF THE ANTIBIOTIC JRNL TITL 2 PEPTIDE DERMADISTINCTIN K BY MULTIDIMENSIONAL SOLUTION AND JRNL TITL 3 ORIENTED 15N AND 31P SOLID-STATE NMR SPECTROSCOPY. JRNL REF BIOPHYS.J. V. 96 2194 2009 JRNL REFN ISSN 0006-3495 JRNL PMID 19289046 JRNL DOI 10.1016/J.BPJ.2008.11.063 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN 2.0, X-PLOR NIH REMARK 3 AUTHORS : BRUKER BIOSPIN (TOPSPIN), SCHWIETERS, KUSZEWSKI, REMARK 3 TJANDRA AND CLORE (X-PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 NOE INTENSITIES WERE CONVERTED INTO SEMI-QUANTITATIVE REMARK 3 DISTANCE RESTRAINS. THE UPPER LIMITS OF THE DISTANCES REMARK 3 RESTRAINS THUS OBTAINED WERE 2.8, 3.4 AND 5.0 A REMARK 3 (STRONG, MEDIUM, AND WEAK NOES RESPECTIVELY). STRUCTURE REMARK 3 CALCULATIONS WERE PERFORMED USING THE XPLOR-NIH SOFTWARE, REMARK 3 VERSION 2.17.0 (SCHWIETERS ET AL., 2003). STARTING WITH REMARK 3 THE EXTENDED STRUCTURE, 500 STRUCTURES WERE GENERATED USING REMARK 3 A SIMULATED ANNEALING PROTOCOL. THIS WAS FOLLOWED BY 20000 REMARK 3 STEPS OF SIMULATED ANNEALING AT 1000 K AND A SUBSEQUENT REMARK 3 DECREASE IN TEMPERATURE IN 15000 STEPS IN THE FIRST REMARK 3 SLOW-COOL ANNEALING STAGE. REMARK 4 REMARK 4 2K9B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-OCT-08. REMARK 100 THE DEPOSITION ID IS D_1000100838. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 318 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 2.0 MM DD K, 400 MM [U-2H] REMARK 210 DPCD38, 400MM DPCD38/H2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H TOCSY; 2D 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, NMRVIEW, X-PLOR NIH, REMARK 210 PROCHECKNMR, MOLMOL REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 500 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY 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 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 LEU A 2 -172.84 -67.77 REMARK 500 1 TRP A 3 -105.40 54.72 REMARK 500 1 SER A 4 142.70 60.31 REMARK 500 1 ALA A 18 -51.77 -29.78 REMARK 500 1 LYS A 19 -70.47 -77.86 REMARK 500 1 ALA A 20 -11.75 -47.58 REMARK 500 1 LYS A 23 -70.13 -41.23 REMARK 500 1 ALA A 28 -71.19 -58.74 REMARK 500 1 ALA A 32 -72.15 -45.26 REMARK 500 2 SER A 4 -140.21 -76.16 REMARK 500 2 LYS A 5 0.15 -68.85 REMARK 500 2 ALA A 18 -51.08 -29.70 REMARK 500 2 LYS A 19 -70.47 -76.92 REMARK 500 2 ALA A 20 -24.07 -39.19 REMARK 500 2 ALA A 32 -107.21 -57.24 REMARK 500 3 TRP A 3 99.14 54.02 REMARK 500 3 SER A 4 -93.84 -156.37 REMARK 500 3 LYS A 5 26.19 -72.65 REMARK 500 3 ALA A 18 -55.19 -29.49 REMARK 500 3 ALA A 20 -17.19 -42.77 REMARK 500 3 ASN A 27 -18.75 -47.06 REMARK 500 3 ALA A 32 -81.02 -62.24 REMARK 500 4 LEU A 2 -73.44 -84.83 REMARK 500 4 TRP A 3 95.60 -43.98 REMARK 500 4 ALA A 21 -72.31 -91.47 REMARK 500 5 SER A 4 -139.63 60.95 REMARK 500 5 LYS A 5 60.06 -103.42 REMARK 500 5 LYS A 7 -83.77 -62.17 REMARK 500 5 ALA A 32 -127.18 -61.40 REMARK 500 6 SER A 4 80.51 -167.41 REMARK 500 6 LYS A 5 70.13 46.65 REMARK 500 6 ALA A 18 -39.56 -29.99 REMARK 500 6 LYS A 19 -76.78 -91.03 REMARK 500 6 ALA A 20 -25.43 -38.15 REMARK 500 6 ALA A 21 -73.79 -90.55 REMARK 500 7 SER A 4 -144.11 -71.13 REMARK 500 7 ALA A 18 -53.64 -29.96 REMARK 500 7 ALA A 21 -66.05 -91.47 REMARK 500 8 LEU A 2 90.92 -171.03 REMARK 500 8 LYS A 5 -104.48 -155.55 REMARK 500 8 ILE A 6 -77.41 57.85 REMARK 500 8 ALA A 18 -55.25 -30.00 REMARK 500 8 ALA A 20 -23.21 -39.35 REMARK 500 8 ALA A 32 -77.50 -47.44 REMARK 500 9 LEU A 2 -56.14 -137.67 REMARK 500 9 TRP A 3 80.08 -57.17 REMARK 500 9 LYS A 23 -70.23 -40.08 REMARK 500 10 LEU A 2 33.17 -75.42 REMARK 500 10 ALA A 18 -54.98 -29.80 REMARK 500 10 ALA A 20 -19.67 -42.37 REMARK 500 REMARK 500 THIS ENTRY HAS 90 RAMACHANDRAN OUTLIERS. 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 34 DBREF 2K9B A 1 33 UNP P83638 DDSK_PHYDS 1 33 SEQADV 2K9B NH2 A 34 UNP P83638 AMIDATION SEQRES 1 A 34 GLY LEU TRP SER LYS ILE LYS ALA ALA GLY LYS GLU ALA SEQRES 2 A 34 ALA LYS ALA ALA ALA LYS ALA ALA GLY LYS ALA ALA LEU SEQRES 3 A 34 ASN ALA VAL SER GLU ALA VAL NH2 HET NH2 A 34 3 HETNAM NH2 AMINO GROUP FORMUL 1 NH2 H2 N HELIX 1 1 LYS A 5 VAL A 33 1 29 LINK C VAL A 33 N NH2 A 34 1555 1555 1.30 SITE 1 AC1 2 ALA A 32 VAL A 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