HEADER ANTIMICROBIAL PROTEIN 21-SEP-22 8GXT TITLE ANTIBACTERIAL PEPTIDE, MEHAMYCIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANTIBACTERIAL PEPTIDE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MELOIDOGYNE HAPLA; SOURCE 3 ORGANISM_TAXID: 6305; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS STRUCTURE FROM XPLOR-NIH, ANTIMICROBIAL PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR N.ISOZUMI,S.OHKI REVDAT 2 30-OCT-24 8GXT 1 REMARK REVDAT 1 27-SEP-23 8GXT 0 JRNL AUTH S.OHKI,N.ISOZUMI JRNL TITL ANTIBACTERIAL PEPTIDE, MEHAMYCIN JRNL REF TO BE PUBLISHED JRNL REFN 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: NULL REMARK 4 REMARK 4 8GXT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-SEP-22. REMARK 100 THE DEPOSITION ID IS D_1300032425. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 4.5 REMARK 210 IONIC STRENGTH : NO REMARK 210 PRESSURE : 1 BAR REMARK 210 SAMPLE CONTENTS : 0.2 MM UNLABELED MEHAMYCIN, 90% REMARK 210 H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-15N NOESY; 3D 1H-15N REMARK 210 TOCSY; 2D 1H-1H NOESY; 2D 1H-1H REMARK 210 TOCSY 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 : SPARKY, CYANA, NMRPIPE REMARK 210 METHOD USED : DGSA-DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 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: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 1 LEU A 3 N LEU A 3 CA 0.121 REMARK 500 1 SER A 4 N SER A 4 CA 0.128 REMARK 500 1 TYR A 7 N TYR A 7 CA 0.124 REMARK 500 1 GLY A 9 N GLY A 9 CA 0.106 REMARK 500 1 CYS A 11 N CYS A 11 CA 0.127 REMARK 500 1 TYR A 12 N TYR A 12 CA 0.132 REMARK 500 1 ILE A 15 N ILE A 15 CA 0.124 REMARK 500 1 ILE A 16 N ILE A 16 CA 0.145 REMARK 500 1 CYS A 18 N CYS A 18 CA 0.126 REMARK 500 1 PHE A 19 N PHE A 19 CA 0.132 REMARK 500 1 ARG A 21 N ARG A 21 CA 0.148 REMARK 500 1 LYS A 24 N LYS A 24 CA 0.131 REMARK 500 1 LYS A 26 N LYS A 26 CA 0.136 REMARK 500 1 LEU A 27 N LEU A 27 CA 0.121 REMARK 500 1 PHE A 28 N PHE A 28 CA 0.136 REMARK 500 1 ASP A 29 N ASP A 29 CA 0.154 REMARK 500 1 HIS A 31 N HIS A 31 CA 0.141 REMARK 500 1 ARG A 32 N ARG A 32 CA 0.146 REMARK 500 1 LYS A 33 N LYS A 33 CA 0.135 REMARK 500 1 LEU A 34 N LEU A 34 CA 0.142 REMARK 500 1 CYS A 35 N CYS A 35 CA 0.127 REMARK 500 1 ILE A 36 N ILE A 36 CA 0.125 REMARK 500 1 LYS A 37 N LYS A 37 CA 0.133 REMARK 500 1 CYS A 39 N CYS A 39 CA 0.133 REMARK 500 1 LYS A 40 N LYS A 40 CA 0.139 REMARK 500 1 GLN A 41 N GLN A 41 CA 0.125 REMARK 500 1 GLY A 43 N GLY A 43 CA 0.110 REMARK 500 1 LYS A 45 N LYS A 45 CA 0.121 REMARK 500 1 GLY A 47 N GLY A 47 CA 0.104 REMARK 500 1 HIS A 48 N HIS A 48 CA 0.121 REMARK 500 1 SER A 50 N SER A 50 CA 0.137 REMARK 500 1 ASN A 51 N ASN A 51 CA 0.140 REMARK 500 1 PHE A 52 N PHE A 52 CA 0.133 REMARK 500 1 LYS A 54 N LYS A 54 CA 0.129 REMARK 500 1 PHE A 55 N PHE A 55 CA 0.129 REMARK 500 1 ARG A 61 N ARG A 61 CA 0.125 REMARK 500 2 LEU A 3 N LEU A 3 CA 0.125 REMARK 500 2 SER A 4 N SER A 4 CA 0.128 REMARK 500 2 GLY A 5 N GLY A 5 CA 0.091 REMARK 500 2 TYR A 7 N TYR A 7 CA 0.123 REMARK 500 2 GLY A 9 N GLY A 9 CA 0.097 REMARK 500 2 GLY A 14 N GLY A 14 CA 0.103 REMARK 500 2 ILE A 16 N ILE A 16 CA 0.147 REMARK 500 2 PHE A 19 N PHE A 19 CA 0.133 REMARK 500 2 ARG A 21 N ARG A 21 CA 0.147 REMARK 500 2 CYS A 23 N CYS A 23 CA 0.147 REMARK 500 2 LYS A 24 N LYS A 24 CA 0.128 REMARK 500 2 LYS A 26 N LYS A 26 CA 0.138 REMARK 500 2 PHE A 28 N PHE A 28 CA 0.142 REMARK 500 2 ASP A 29 N ASP A 29 CA 0.146 REMARK 500 REMARK 500 THIS ENTRY HAS 689 BOND DEVIATIONS. 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 SER A 4 -171.84 48.07 REMARK 500 1 LYS A 6 -68.08 -121.94 REMARK 500 1 TYR A 12 -136.69 49.78 REMARK 500 1 PHE A 13 32.26 -149.41 REMARK 500 1 ILE A 15 -29.98 -157.13 REMARK 500 1 CYS A 18 120.94 58.96 REMARK 500 1 PHE A 19 -44.15 -161.58 REMARK 500 1 VAL A 20 -153.86 -131.37 REMARK 500 1 LYS A 26 154.68 61.57 REMARK 500 1 LEU A 27 109.51 59.74 REMARK 500 1 ASP A 29 -46.71 77.96 REMARK 500 1 LYS A 45 -11.08 -157.48 REMARK 500 1 SER A 50 31.96 -174.20 REMARK 500 1 PHE A 52 19.49 55.42 REMARK 500 1 LYS A 54 33.07 -172.35 REMARK 500 1 PHE A 55 -36.80 -157.43 REMARK 500 2 TYR A 7 164.28 61.90 REMARK 500 2 TYR A 12 -99.98 -132.70 REMARK 500 2 PHE A 13 20.02 -154.79 REMARK 500 2 ILE A 15 -45.68 56.75 REMARK 500 2 PHE A 19 -43.19 -164.83 REMARK 500 2 VAL A 20 -153.71 -132.95 REMARK 500 2 LYS A 26 158.59 61.59 REMARK 500 2 LEU A 27 103.82 52.25 REMARK 500 2 ASP A 29 -42.04 80.08 REMARK 500 2 LYS A 45 -41.45 -134.25 REMARK 500 2 SER A 50 21.01 -163.17 REMARK 500 2 LYS A 54 36.45 -174.69 REMARK 500 2 PHE A 55 -38.48 -157.76 REMARK 500 3 TYR A 12 -98.95 -121.32 REMARK 500 3 PHE A 13 34.63 -172.23 REMARK 500 3 ILE A 15 -39.66 -160.96 REMARK 500 3 PHE A 19 -60.32 -153.17 REMARK 500 3 ARG A 21 -65.90 57.35 REMARK 500 3 CYS A 23 -69.16 63.71 REMARK 500 3 LYS A 26 157.53 61.27 REMARK 500 3 LEU A 27 108.98 59.43 REMARK 500 3 ASP A 29 -44.25 78.48 REMARK 500 3 LYS A 45 -23.01 -142.64 REMARK 500 3 SER A 50 25.95 -164.11 REMARK 500 3 PHE A 53 -70.76 -115.77 REMARK 500 3 LYS A 54 32.42 -176.05 REMARK 500 4 SER A 4 143.36 48.87 REMARK 500 4 ILE A 15 -17.86 -152.91 REMARK 500 4 CYS A 18 127.51 65.74 REMARK 500 4 PHE A 19 -59.77 -154.22 REMARK 500 4 ARG A 21 -69.89 54.90 REMARK 500 4 CYS A 23 42.16 -103.03 REMARK 500 4 LYS A 24 -57.93 -144.61 REMARK 500 4 LYS A 26 175.55 59.67 REMARK 500 REMARK 500 THIS ENTRY HAS 286 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 21 0.31 SIDE CHAIN REMARK 500 1 ARG A 32 0.29 SIDE CHAIN REMARK 500 1 ARG A 61 0.30 SIDE CHAIN REMARK 500 2 ARG A 21 0.33 SIDE CHAIN REMARK 500 2 ARG A 32 0.33 SIDE CHAIN REMARK 500 2 ARG A 61 0.30 SIDE CHAIN REMARK 500 3 ARG A 21 0.31 SIDE CHAIN REMARK 500 3 ARG A 32 0.33 SIDE CHAIN REMARK 500 3 ARG A 61 0.30 SIDE CHAIN REMARK 500 4 ARG A 21 0.32 SIDE CHAIN REMARK 500 4 ARG A 32 0.31 SIDE CHAIN REMARK 500 4 ARG A 61 0.33 SIDE CHAIN REMARK 500 5 ARG A 21 0.33 SIDE CHAIN REMARK 500 5 ARG A 32 0.32 SIDE CHAIN REMARK 500 5 ARG A 61 0.32 SIDE CHAIN REMARK 500 6 ARG A 21 0.33 SIDE CHAIN REMARK 500 6 ARG A 32 0.29 SIDE CHAIN REMARK 500 6 ARG A 61 0.31 SIDE CHAIN REMARK 500 7 ARG A 21 0.32 SIDE CHAIN REMARK 500 7 ARG A 32 0.29 SIDE CHAIN REMARK 500 7 ARG A 61 0.33 SIDE CHAIN REMARK 500 8 ARG A 21 0.32 SIDE CHAIN REMARK 500 8 ARG A 32 0.31 SIDE CHAIN REMARK 500 8 ARG A 61 0.32 SIDE CHAIN REMARK 500 9 ARG A 21 0.33 SIDE CHAIN REMARK 500 9 ARG A 32 0.31 SIDE CHAIN REMARK 500 9 ARG A 61 0.31 SIDE CHAIN REMARK 500 10 ARG A 21 0.33 SIDE CHAIN REMARK 500 10 ARG A 32 0.32 SIDE CHAIN REMARK 500 10 ARG A 61 0.31 SIDE CHAIN REMARK 500 11 ARG A 21 0.33 SIDE CHAIN REMARK 500 11 ARG A 32 0.31 SIDE CHAIN REMARK 500 11 ARG A 61 0.31 SIDE CHAIN REMARK 500 12 ARG A 21 0.30 SIDE CHAIN REMARK 500 12 ARG A 32 0.32 SIDE CHAIN REMARK 500 12 ARG A 61 0.33 SIDE CHAIN REMARK 500 13 ARG A 21 0.32 SIDE CHAIN REMARK 500 13 ARG A 32 0.31 SIDE CHAIN REMARK 500 13 ARG A 61 0.30 SIDE CHAIN REMARK 500 14 ARG A 21 0.31 SIDE CHAIN REMARK 500 14 ARG A 32 0.26 SIDE CHAIN REMARK 500 14 ARG A 61 0.30 SIDE CHAIN REMARK 500 15 ARG A 21 0.29 SIDE CHAIN REMARK 500 15 ARG A 32 0.29 SIDE CHAIN REMARK 500 15 ARG A 61 0.32 SIDE CHAIN REMARK 500 16 ARG A 21 0.29 SIDE CHAIN REMARK 500 16 ARG A 32 0.32 SIDE CHAIN REMARK 500 16 ARG A 61 0.33 SIDE CHAIN REMARK 500 17 ARG A 21 0.33 SIDE CHAIN REMARK 500 17 ARG A 32 0.29 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 60 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36511 RELATED DB: BMRB REMARK 900 ANTIBACTERIAL PEPTIDE, MEHAMYCIN DBREF1 8GXT A 8 61 UNP A0A1I8C2Q5_MELHA DBREF2 8GXT A A0A1I8C2Q5 47 100 SEQADV 8GXT ASP A 1 UNP A0A1I8C2Q EXPRESSION TAG SEQADV 8GXT VAL A 2 UNP A0A1I8C2Q EXPRESSION TAG SEQADV 8GXT LEU A 3 UNP A0A1I8C2Q EXPRESSION TAG SEQADV 8GXT SER A 4 UNP A0A1I8C2Q EXPRESSION TAG SEQADV 8GXT GLY A 5 UNP A0A1I8C2Q EXPRESSION TAG SEQADV 8GXT LYS A 6 UNP A0A1I8C2Q EXPRESSION TAG SEQADV 8GXT TYR A 7 UNP A0A1I8C2Q EXPRESSION TAG SEQRES 1 A 61 ASP VAL LEU SER GLY LYS TYR LYS GLY PRO CYS TYR PHE SEQRES 2 A 61 GLY ILE ILE PRO CYS PHE VAL ARG GLY CYS LYS PRO LYS SEQRES 3 A 61 LEU PHE ASP ALA HIS ARG LYS LEU CYS ILE LYS LEU CYS SEQRES 4 A 61 LYS GLN GLU GLY PHE LYS SER GLY HIS CYS SER ASN PHE SEQRES 5 A 61 PHE LYS PHE GLN CYS TRP CYS THR ARG HELIX 1 AA1 ALA A 30 GLN A 41 1 12 SHEET 1 AA1 2 SER A 46 HIS A 48 0 SHEET 2 AA1 2 TRP A 58 THR A 60 -1 O THR A 60 N SER A 46 SSBOND 1 CYS A 11 CYS A 49 1555 1555 2.04 SSBOND 2 CYS A 18 CYS A 23 1555 1555 2.02 SSBOND 3 CYS A 35 CYS A 57 1555 1555 2.05 SSBOND 4 CYS A 39 CYS A 59 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 MODEL 1