HEADER ANTIMICROBIAL PROTEIN 08-NOV-07 2JX6 TITLE STRUCTURE AND MEMBRANE INTERACTIONS OF THE ANTIBIOTIC PEPTIDE TITLE 2 DERMADISTINCTIN K BY SOLUTION AND ORIENTED 15N AND 31P SOLID-STATE TITLE 3 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 ORGANISM_SCIENTIFIC: PHYLLOMEDUSA DISTINCTA; SOURCE 4 ORGANISM_COMMON: MONKEY FROG; SOURCE 5 ORGANISM_TAXID: 164618; SOURCE 6 OTHER_DETAILS: THE PEPTIDE WAS SYNTHESIZED BY SOLID-PHASE SYNTHESIS SOURCE 7 USING FMOC CHEMISTRY. THE PEPTIDE IS AN ANTIMICROBIAL PEPTIDE THAT SOURCE 8 IS NATURALLY FOUND FROM THE SKIN SECRETION OF PHYLLOMEDUSA SOURCE 9 DISTINCTA, A FROG SPECIES FOUND IN BRAZILIAN FORESTS. KEYWDS ALPHA HELIX, AMPHIPATHIC CHARACTER, C-TERMINAL CARBOXYAMIDATION, KEYWDS 2 MEMBRANE PEPTIDE, AMPHIBIAN DEFENSE PEPTIDE, ANTIBIOTIC, KEYWDS 3 ANTIMICROBIAL, SECRETED, ANTIMICROBIAL PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR C.MENDONCA MORAES,R.M.VERLY,J.M.RESENDE,M.P.BEMQUERER,D.PILO-VELOSO, AUTHOR 2 A.VALENTE,F.C.L.ALMEIDA,B.BECHINGER REVDAT 5 20-NOV-24 2JX6 1 REMARK REVDAT 4 16-MAR-22 2JX6 1 REMARK LINK REVDAT 3 31-MAR-09 2JX6 1 JRNL REVDAT 2 24-FEB-09 2JX6 1 VERSN REVDAT 1 11-NOV-08 2JX6 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 : XWINNMR, X-PLOR NIH 2.17.0 REMARK 3 AUTHORS : BRUKER BIOSPIN (XWINNMR), 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 DISTANCES REMARK 3 RESTRAINS. THE UPPER LIMITS OF THE DISTANCES THUS OBTAINED WERE REMARK 3 2.8, 3.4 AND 5.0A; (FOR STRONG, MEDIUM, AND WEAK NOES, REMARK 3 RESPECTIVELY). STRUCTURE CALCULATIONS WERE PERFORMED USING THE REMARK 3 XPLOR-NIH SOFTWARE, VERSION 2.17.0 . STARTING WITH THE EXTENDED REMARK 3 STRUCTURE, 500 STRUCTURES WERE GENERATED USING A SIMULATED REMARK 3 ANNEALING PROTOCOL. THIS WAS FOLLOWED BY 20000 STEPS OF SIMULATED REMARK 3 ANNEALING AT 1000 K AND A SUBSEQUENT DECREASE IN TEMPERA REMARK 3 URE IN 15000 STEPS IN THE FIRST SLOW-COOL ANNEALING STAGE. REMARK 4 REMARK 4 2JX6 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-NOV-07. REMARK 100 THE DEPOSITION ID IS D_1000100402. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293.15 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 2.0MM DERMADISTINCTIN K; REMARK 210 TRIFLUOROETHANOL; H2O 60%, D2O REMARK 210 40% REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H TOCSY; 2D 1H-1H NOESY; REMARK 210 2D 1H-13C HSQC; 2D 1H-15N HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, NMRVIEW 5.0.4, X-PLOR REMARK 210 NIH 2.17.0, MOLMOL 2K.2, REMARK 210 PROCHECK 3.5.4 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: 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 TRP A 3 31.64 -98.77 REMARK 500 1 SER A 4 -171.56 52.16 REMARK 500 1 LYS A 5 -47.11 -162.80 REMARK 500 1 ILE A 6 66.33 -117.26 REMARK 500 1 ALA A 13 -75.37 -60.37 REMARK 500 1 ALA A 16 -62.82 179.54 REMARK 500 2 ALA A 13 -76.76 -55.03 REMARK 500 2 ALA A 16 -62.59 -175.74 REMARK 500 3 TRP A 3 77.06 -67.53 REMARK 500 3 ALA A 13 -90.47 -58.10 REMARK 500 3 LYS A 15 77.32 -162.45 REMARK 500 3 ALA A 16 -62.75 177.18 REMARK 500 4 TRP A 3 39.97 -160.26 REMARK 500 4 SER A 4 48.00 -148.47 REMARK 500 4 ALA A 13 -80.83 -52.04 REMARK 500 4 ALA A 16 -63.56 -179.60 REMARK 500 5 TRP A 3 91.24 -167.33 REMARK 500 5 SER A 4 -47.95 -141.99 REMARK 500 5 ALA A 13 -77.96 -51.75 REMARK 500 5 LYS A 15 54.14 -170.44 REMARK 500 5 ALA A 16 -63.19 -176.87 REMARK 500 6 SER A 4 74.71 -113.09 REMARK 500 6 ALA A 13 -81.30 -52.74 REMARK 500 6 ALA A 16 -62.78 178.60 REMARK 500 7 LYS A 5 -42.08 -165.54 REMARK 500 7 ALA A 13 -92.30 -52.47 REMARK 500 7 LYS A 15 76.13 -68.36 REMARK 500 7 ALA A 16 -63.01 176.79 REMARK 500 8 SER A 4 45.48 -164.14 REMARK 500 8 ILE A 6 56.14 -104.26 REMARK 500 8 LYS A 7 -68.57 -100.77 REMARK 500 8 ALA A 13 -73.17 -60.94 REMARK 500 8 LYS A 15 52.86 -90.85 REMARK 500 8 ALA A 16 -63.17 -179.40 REMARK 500 9 LYS A 5 -158.70 -69.71 REMARK 500 9 ALA A 13 -77.28 -52.94 REMARK 500 9 ALA A 16 -63.31 -179.55 REMARK 500 10 TRP A 3 41.31 -95.89 REMARK 500 10 LYS A 5 -63.85 -101.43 REMARK 500 10 ALA A 13 -75.22 -52.81 REMARK 500 10 ALA A 16 -61.95 179.35 REMARK 500 10 ALA A 28 -59.23 -136.54 REMARK 500 11 LYS A 5 -172.63 53.31 REMARK 500 11 ALA A 13 -80.78 -52.50 REMARK 500 11 ALA A 16 -62.91 178.50 REMARK 500 12 ILE A 6 65.47 -108.15 REMARK 500 12 LYS A 7 -55.27 -129.71 REMARK 500 12 ALA A 13 -76.56 -52.46 REMARK 500 12 ALA A 16 -62.21 178.03 REMARK 500 13 TRP A 3 88.45 52.44 REMARK 500 REMARK 500 THIS ENTRY HAS 82 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL DBREF 2JX6 A 1 33 UNP P83638 DDSK_PHYDS 1 33 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 7 VAL A 33 1 27 LINK C VAL A 33 N NH2 A 34 1555 1555 1.31 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 465 N NH2 A 34 26.519 1.145 -8.663 1.00 0.00 N HETATM 466 HN1 NH2 A 34 25.601 1.404 -8.420 1.00 0.00 H HETATM 467 HN2 NH2 A 34 27.069 1.736 -9.228 1.00 0.00 H TER 468 NH2 A 34 ENDMDL MODEL 2 HETATM 465 N NH2 A 34 26.124 2.294 -8.122 1.00 0.00 N HETATM 466 HN1 NH2 A 34 25.185 2.197 -7.849 1.00 0.00 H HETATM 467 HN2 NH2 A 34 26.411 3.083 -8.640 1.00 0.00 H TER 468 NH2 A 34 ENDMDL MODEL 3 HETATM 465 N NH2 A 34 26.866 1.183 -8.446 1.00 0.00 N HETATM 466 HN1 NH2 A 34 25.889 1.134 -8.351 1.00 0.00 H HETATM 467 HN2 NH2 A 34 27.278 1.921 -8.957 1.00 0.00 H TER 468 NH2 A 34 ENDMDL MODEL 4 HETATM 465 N NH2 A 34 25.917 1.169 -8.421 1.00 0.00 N HETATM 466 HN1 NH2 A 34 25.264 1.411 -7.728 1.00 0.00 H HETATM 467 HN2 NH2 A 34 26.130 1.793 -9.153 1.00 0.00 H TER 468 NH2 A 34 ENDMDL MODEL 5 HETATM 465 N NH2 A 34 26.188 0.860 -8.659 1.00 0.00 N HETATM 466 HN1 NH2 A 34 25.263 0.967 -8.345 1.00 0.00 H HETATM 467 HN2 NH2 A 34 26.532 1.424 -9.391 1.00 0.00 H TER 468 NH2 A 34 ENDMDL MODEL 6 HETATM 465 N NH2 A 34 25.159 4.991 -9.856 1.00 0.00 N HETATM 466 HN1 NH2 A 34 24.193 4.804 -9.882 1.00 0.00 H HETATM 467 HN2 NH2 A 34 25.495 5.893 -10.069 1.00 0.00 H TER 468 NH2 A 34 ENDMDL MODEL 7 HETATM 465 N NH2 A 34 26.065 -0.078 -7.959 1.00 0.00 N HETATM 466 HN1 NH2 A 34 25.090 -0.126 -7.842 1.00 0.00 H HETATM 467 HN2 NH2 A 34 26.448 0.382 -8.744 1.00 0.00 H TER 468 NH2 A 34 ENDMDL MODEL 8 HETATM 465 N NH2 A 34 26.437 1.061 -7.810 1.00 0.00 N HETATM 466 HN1 NH2 A 34 25.693 1.556 -7.401 1.00 0.00 H HETATM 467 HN2 NH2 A 34 26.945 1.456 -8.557 1.00 0.00 H TER 468 NH2 A 34 ENDMDL MODEL 9 HETATM 465 N NH2 A 34 26.144 1.645 -7.233 1.00 0.00 N HETATM 466 HN1 NH2 A 34 25.183 1.651 -7.026 1.00 0.00 H HETATM 467 HN2 NH2 A 34 26.492 2.182 -7.983 1.00 0.00 H TER 468 NH2 A 34 ENDMDL MODEL 10 HETATM 465 N NH2 A 34 25.157 -2.042 -10.026 1.00 0.00 N HETATM 466 HN1 NH2 A 34 24.247 -2.402 -9.937 1.00 0.00 H HETATM 467 HN2 NH2 A 34 25.417 -1.548 -10.840 1.00 0.00 H TER 468 NH2 A 34 ENDMDL MODEL 11 HETATM 465 N NH2 A 34 26.086 3.066 -8.383 1.00 0.00 N HETATM 466 HN1 NH2 A 34 25.456 2.994 -7.632 1.00 0.00 H HETATM 467 HN2 NH2 A 34 26.190 3.920 -8.863 1.00 0.00 H TER 468 NH2 A 34 ENDMDL MODEL 12 HETATM 465 N NH2 A 34 25.676 4.634 -9.689 1.00 0.00 N HETATM 466 HN1 NH2 A 34 24.695 4.570 -9.690 1.00 0.00 H HETATM 467 HN2 NH2 A 34 26.116 5.507 -9.809 1.00 0.00 H TER 468 NH2 A 34 ENDMDL MODEL 13 HETATM 465 N NH2 A 34 24.888 1.607 -10.334 1.00 0.00 N HETATM 466 HN1 NH2 A 34 24.353 1.732 -9.519 1.00 0.00 H HETATM 467 HN2 NH2 A 34 25.171 2.388 -10.865 1.00 0.00 H TER 468 NH2 A 34 ENDMDL MODEL 14 HETATM 465 N NH2 A 34 26.802 0.808 -8.836 1.00 0.00 N HETATM 466 HN1 NH2 A 34 26.161 1.073 -8.141 1.00 0.00 H HETATM 467 HN2 NH2 A 34 27.088 1.457 -9.520 1.00 0.00 H TER 468 NH2 A 34 ENDMDL MODEL 15 HETATM 465 N NH2 A 34 27.099 1.984 -8.565 1.00 0.00 N HETATM 466 HN1 NH2 A 34 26.501 2.240 -7.828 1.00 0.00 H HETATM 467 HN2 NH2 A 34 27.399 2.659 -9.218 1.00 0.00 H TER 468 NH2 A 34 ENDMDL MODEL 16 HETATM 465 N NH2 A 34 25.967 1.625 -9.344 1.00 0.00 N HETATM 466 HN1 NH2 A 34 24.992 1.525 -9.283 1.00 0.00 H HETATM 467 HN2 NH2 A 34 26.359 2.326 -9.916 1.00 0.00 H TER 468 NH2 A 34 ENDMDL MODEL 17 HETATM 465 N NH2 A 34 27.182 0.127 -5.383 1.00 0.00 N HETATM 466 HN1 NH2 A 34 26.320 0.575 -5.231 1.00 0.00 H HETATM 467 HN2 NH2 A 34 27.724 0.351 -6.175 1.00 0.00 H TER 468 NH2 A 34 ENDMDL MODEL 18 HETATM 465 N NH2 A 34 27.759 3.331 -5.747 1.00 0.00 N HETATM 466 HN1 NH2 A 34 26.835 3.382 -6.079 1.00 0.00 H HETATM 467 HN2 NH2 A 34 28.380 4.084 -5.884 1.00 0.00 H TER 468 NH2 A 34 ENDMDL MODEL 19 HETATM 465 N NH2 A 34 26.336 1.189 -9.606 1.00 0.00 N HETATM 466 HN1 NH2 A 34 25.833 1.522 -8.831 1.00 0.00 H HETATM 467 HN2 NH2 A 34 26.953 1.786 -10.090 1.00 0.00 H TER 468 NH2 A 34 ENDMDL MODEL 20 HETATM 465 N NH2 A 34 26.567 -4.508 -6.547 1.00 0.00 N HETATM 466 HN1 NH2 A 34 25.741 -4.910 -6.197 1.00 0.00 H HETATM 467 HN2 NH2 A 34 27.436 -4.953 -6.404 1.00 0.00 H TER 468 NH2 A 34 ENDMDL CONECT 451 465 CONECT 465 451 466 467 CONECT 466 465 CONECT 467 465 MASTER 148 0 1 1 0 0 0 6 222 1 4 3 END