PDB Short entry for 1XV3 HEADER ANTIBIOTIC 27-OCT-04 1XV3 TITLE NMR STRUCTURE OF THE SYNTHETIC PENAEIDIN 4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PENAEIDIN-4D; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PEN-4D; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THE MOLECULE HAS BEEN SYNTHESIZED BY USING THE NATIVE SOURCE 4 LIGATION METHODOLOGY KEYWDS ANTIMICROBIAL PEPTIDE, ANTIFUNGAL PEPTIDE, CYSTEINE-RICH, DISULFIDE KEYWDS 2 BOND, OXIDATIVE FOLDING, PENAEIDIN, PROLINE-RICH, SHRIMP, ANTIBIOTIC EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR B.J.CUTHBERTSON,Y.YANG,E.E.BULLESBACH,E.BACHERE,P.S.GROSS,A.AUMELAS REVDAT 4 02-MAR-22 1XV3 1 REMARK REVDAT 3 24-FEB-09 1XV3 1 VERSN REVDAT 2 26-APR-05 1XV3 1 JRNL REVDAT 1 15-FEB-05 1XV3 0 JRNL AUTH B.J.CUTHBERTSON,Y.YANG,E.BACHERE,E.E.BULLESBACH,P.S.GROSS, JRNL AUTH 2 A.AUMELAS JRNL TITL SOLUTION STRUCTURE OF SYNTHETIC PENAEIDIN-4 WITH STRUCTURAL JRNL TITL 2 AND FUNCTIONAL COMPARISONS TO PENAEIDIN-3 JRNL REF J.BIOL.CHEM. V. 280 16009 2005 JRNL REFN ISSN 0021-9258 JRNL PMID 15699044 JRNL DOI 10.1074/JBC.M412420200 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.8, X-PLOR 3.8 REMARK 3 AUTHORS : RICE, L.M. AND BRUNGER, A.T. (X-PLOR), BRUNGER (X REMARK 3 -PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1XV3 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-OCT-04. REMARK 100 THE DEPOSITION ID IS D_1000030797. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 3.6 REMARK 210 IONIC STRENGTH : NO SALT WAS ADDED REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM, PH 3.6; 1MM, PH 3.6 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : DQF-COSY TOCSY NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 3.1, GIFA 4, INSIGHT REMARK 210 INSIGHT97 REMARK 210 METHOD USED : DISTANCE GEOMETRY, SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 40 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: DATA SETS RECORDED AT THREE TEMPERATURES ( 285, 293 AND REMARK 210 298 K) WERE USED FOR THE ASSIGNMENT. THIS STRUCTURE WAS REMARK 210 DETERMINED USING STANDARD 2D HOMONUCLEAR TECHNIQUES. 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 ARG A 7 72.66 -152.60 REMARK 500 1 PRO A 12 -166.78 -78.22 REMARK 500 1 CYS A 45 -60.47 -90.31 REMARK 500 2 SER A 2 79.00 56.86 REMARK 500 2 TYR A 5 156.28 68.13 REMARK 500 2 SER A 13 63.40 -105.54 REMARK 500 2 ARG A 40 -60.21 -98.18 REMARK 500 3 PRO A 12 -156.13 -75.27 REMARK 500 3 SER A 13 171.93 -58.09 REMARK 500 3 PHE A 17 -179.20 -62.43 REMARK 500 3 ILE A 18 -177.82 -60.64 REMARK 500 4 SER A 3 116.63 64.42 REMARK 500 4 PRO A 12 -165.88 -77.98 REMARK 500 4 ARG A 14 134.72 66.78 REMARK 500 5 ARG A 10 135.15 -171.53 REMARK 500 5 PRO A 12 -164.35 -78.21 REMARK 500 5 CYS A 45 -60.37 -90.88 REMARK 500 6 ARG A 7 81.44 54.95 REMARK 500 6 ARG A 14 148.44 178.48 REMARK 500 6 PHE A 17 163.94 61.47 REMARK 500 7 SER A 2 76.37 -152.34 REMARK 500 7 TYR A 5 85.05 52.78 REMARK 500 7 ARG A 7 131.18 67.29 REMARK 500 7 PRO A 12 -160.11 -75.68 REMARK 500 8 SER A 2 174.60 62.65 REMARK 500 8 TYR A 5 142.34 67.86 REMARK 500 8 PRO A 12 -160.95 -77.54 REMARK 500 9 THR A 6 54.23 -106.49 REMARK 500 9 ARG A 7 121.52 62.97 REMARK 500 9 ARG A 10 92.33 60.19 REMARK 500 9 PRO A 12 -159.31 -79.06 REMARK 500 9 ARG A 14 108.69 -48.16 REMARK 500 10 SER A 2 76.90 57.42 REMARK 500 10 TYR A 5 114.51 66.89 REMARK 500 10 PRO A 12 -162.21 -77.73 REMARK 500 10 ARG A 14 136.33 67.44 REMARK 500 10 HIS A 46 54.81 -96.43 REMARK 500 11 LYS A 11 80.19 57.89 REMARK 500 11 PRO A 12 -161.99 -75.90 REMARK 500 11 SER A 13 36.22 -97.77 REMARK 500 11 ARG A 14 142.81 64.13 REMARK 500 11 ILE A 18 -171.53 -68.43 REMARK 500 12 SER A 3 77.86 56.44 REMARK 500 12 THR A 6 164.32 63.24 REMARK 500 12 ARG A 10 92.53 -68.31 REMARK 500 12 LYS A 11 86.46 -154.99 REMARK 500 12 PRO A 12 -163.39 -77.17 REMARK 500 13 ARG A 10 160.08 65.80 REMARK 500 13 PRO A 12 -160.23 -74.37 REMARK 500 14 TYR A 5 101.88 63.93 REMARK 500 REMARK 500 THIS ENTRY HAS 76 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 ARG A 7 0.32 SIDE CHAIN REMARK 500 1 ARG A 10 0.29 SIDE CHAIN REMARK 500 1 ARG A 14 0.32 SIDE CHAIN REMARK 500 1 ARG A 19 0.23 SIDE CHAIN REMARK 500 1 ARG A 35 0.26 SIDE CHAIN REMARK 500 1 ARG A 40 0.31 SIDE CHAIN REMARK 500 2 ARG A 7 0.29 SIDE CHAIN REMARK 500 2 ARG A 10 0.29 SIDE CHAIN REMARK 500 2 ARG A 14 0.29 SIDE CHAIN REMARK 500 2 ARG A 19 0.31 SIDE CHAIN REMARK 500 2 ARG A 35 0.32 SIDE CHAIN REMARK 500 2 ARG A 40 0.32 SIDE CHAIN REMARK 500 3 ARG A 7 0.32 SIDE CHAIN REMARK 500 3 ARG A 10 0.32 SIDE CHAIN REMARK 500 3 ARG A 14 0.32 SIDE CHAIN REMARK 500 3 ARG A 19 0.32 SIDE CHAIN REMARK 500 3 ARG A 35 0.31 SIDE CHAIN REMARK 500 3 ARG A 40 0.31 SIDE CHAIN REMARK 500 4 ARG A 7 0.29 SIDE CHAIN REMARK 500 4 ARG A 10 0.32 SIDE CHAIN REMARK 500 4 ARG A 14 0.31 SIDE CHAIN REMARK 500 4 ARG A 19 0.32 SIDE CHAIN REMARK 500 4 ARG A 35 0.31 SIDE CHAIN REMARK 500 4 ARG A 40 0.31 SIDE CHAIN REMARK 500 5 ARG A 7 0.29 SIDE CHAIN REMARK 500 5 ARG A 10 0.30 SIDE CHAIN REMARK 500 5 ARG A 14 0.32 SIDE CHAIN REMARK 500 5 ARG A 19 0.30 SIDE CHAIN REMARK 500 5 ARG A 35 0.29 SIDE CHAIN REMARK 500 5 ARG A 40 0.31 SIDE CHAIN REMARK 500 6 ARG A 7 0.31 SIDE CHAIN REMARK 500 6 ARG A 10 0.32 SIDE CHAIN REMARK 500 6 ARG A 14 0.32 SIDE CHAIN REMARK 500 6 ARG A 19 0.20 SIDE CHAIN REMARK 500 6 ARG A 35 0.31 SIDE CHAIN REMARK 500 6 ARG A 40 0.32 SIDE CHAIN REMARK 500 7 ARG A 7 0.28 SIDE CHAIN REMARK 500 7 ARG A 10 0.32 SIDE CHAIN REMARK 500 7 ARG A 14 0.31 SIDE CHAIN REMARK 500 7 ARG A 19 0.29 SIDE CHAIN REMARK 500 7 ARG A 35 0.32 SIDE CHAIN REMARK 500 7 ARG A 40 0.30 SIDE CHAIN REMARK 500 8 ARG A 7 0.32 SIDE CHAIN REMARK 500 8 ARG A 10 0.31 SIDE CHAIN REMARK 500 8 ARG A 14 0.32 SIDE CHAIN REMARK 500 8 ARG A 19 0.32 SIDE CHAIN REMARK 500 8 ARG A 35 0.32 SIDE CHAIN REMARK 500 8 ARG A 40 0.31 SIDE CHAIN REMARK 500 9 ARG A 7 0.32 SIDE CHAIN REMARK 500 9 ARG A 10 0.32 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 120 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1XV3 A 1 47 UNP Q962A7 PEN4D_LITSE 20 66 SEQRES 1 A 47 HIS SER SER GLY TYR THR ARG PRO LEU ARG LYS PRO SER SEQRES 2 A 47 ARG PRO ILE PHE ILE ARG PRO ILE GLY CYS ASP VAL CYS SEQRES 3 A 47 TYR GLY ILE PRO SER SER THR ALA ARG LEU CYS CYS PHE SEQRES 4 A 47 ARG TYR GLY ASP CYS CYS HIS LEU HELIX 1 1 PRO A 30 ARG A 40 1 11 SSBOND 1 CYS A 23 CYS A 37 1555 1555 2.02 SSBOND 2 CYS A 26 CYS A 44 1555 1555 2.02 SSBOND 3 CYS A 38 CYS A 45 1555 1555 2.02 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