10 20 30 40 50 60 70 80 2K9B - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER ANTIBIOTIC 07-OCT-08 2K9B
TITLE STRUCTURE AND MEMBRANE INTERACTIONS OF THE ANTIBIOTIC TITLE 2 PEPTIDE DERMADISTINCTIN K BY MULTIDIMENSIONAL SOLUTION AND TITLE 3 ORIENTED 15N AND 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 SOURCE 4 SYNTHESIS USING FMOC CHEMISTRY
KEYWDS AMPHIPATHIC ALPHA-HELIX, MEMBRANE PROTEIN STRUCTURE KEYWDS 2 DETERMINATION, C-TERMINAL CARBOXYAMIDATION, ANTIMICROBIAL KEYWDS 3 PROTEIN, AMPHIBIAN DEFENSE PEPTIDE, ANTIBIOTIC, KEYWDS 4 ANTIMICROBIAL, SECRETED
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR C.M.MORAES,R.M.VERLY,J.M.RESENDE,C.AISENBREY,M.P.BEMQUERER, AUTHOR 2 D.PILO-VELOSO,A.VALENTE,F.C.L.ALMEIDA,B.BECHINGER
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, JRNL AUTH 3 F.C.L.ALMEIDA,B.BECHINGER JRNL TITL STRUCTURE AND MEMBRANE INTERACTIONS OF THE JRNL TITL 2 ANTIBIOTIC PEPTIDE DERMADISTINCTIN K BY JRNL TITL 3 MULTIDIMENSIONAL SOLUTION AND ORIENTED 15N AND 31P JRNL TITL 4 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 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR_NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE 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. 3.20, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-OCT-08. REMARK 100 THE RCSB ID CODE IS RCSB100838.
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 : TOPSPIN 2.0, NMRPIPE, REMARK 210 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 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 11 LEU A 2 -61.30 -90.09 REMARK 500 11 ALA A 18 -53.35 -29.95 REMARK 500 11 LYS A 19 -70.72 -77.29 REMARK 500 11 ALA A 20 -19.66 -41.90 REMARK 500 12 LYS A 5 62.31 31.27 REMARK 500 12 LYS A 19 -70.43 -78.50 REMARK 500 12 LYS A 23 -70.16 -42.55 REMARK 500 13 LEU A 2 76.57 -60.34 REMARK 500 13 TRP A 3 -43.42 -163.99 REMARK 500 13 LYS A 5 40.84 -165.12 REMARK 500 13 ALA A 8 -70.86 -44.09 REMARK 500 13 ALA A 21 -67.78 -91.43 REMARK 500 13 ALA A 32 -86.99 -44.06 REMARK 500 14 ALA A 18 -56.97 -29.94 REMARK 500 14 LYS A 23 -70.70 -47.27 REMARK 500 15 LEU A 2 17.11 50.05 REMARK 500 15 SER A 4 53.24 -90.11 REMARK 500 15 ALA A 18 -52.80 -29.91 REMARK 500 15 LYS A 19 -71.05 -78.63 REMARK 500 15 ALA A 20 -16.26 -43.75 REMARK 500 15 ALA A 32 -80.07 -48.49 REMARK 500 16 TRP A 3 73.40 48.95 REMARK 500 16 SER A 4 -59.74 -149.62 REMARK 500 16 LYS A 7 -82.13 -79.98 REMARK 500 16 ALA A 18 -54.29 -29.99 REMARK 500 16 ALA A 20 -16.28 -43.42 REMARK 500 17 LYS A 5 7.25 -67.69 REMARK 500 17 LYS A 19 -70.72 -77.36 REMARK 500 18 LEU A 2 -98.93 -74.40 REMARK 500 18 SER A 4 -27.53 173.83 REMARK 500 18 ALA A 18 -55.54 -29.89 REMARK 500 18 ALA A 20 -17.67 -44.14 REMARK 500 19 TRP A 3 61.28 -161.20 REMARK 500 19 SER A 4 -62.93 -90.18 REMARK 500 19 LYS A 5 54.10 -161.11 REMARK 500 19 ALA A 18 -52.01 -29.87 REMARK 500 19 LYS A 19 -71.75 -77.60 REMARK 500 19 ALA A 20 -18.51 -42.44 REMARK 500 19 ALA A 21 -71.46 -87.34 REMARK 500 20 ALA A 18 -54.30 -29.81 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