1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Loth, K. Asokan, A. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic C3 H7 N O2 89.093 y ALANINE L-peptide linking C6 H15 N4 O2 1 175.209 y ARGININE L-peptide linking C4 H8 N2 O3 132.118 y ASPARAGINE L-peptide linking C4 H7 N O4 133.103 y ASPARTIC ACID L-peptide linking C3 H7 N O2 S 121.158 y CYSTEINE L-peptide linking C5 H10 N2 O3 146.144 y GLUTAMINE L-peptide linking C5 H9 N O4 147.129 y GLUTAMIC ACID L-peptide linking C2 H5 N O2 75.067 y GLYCINE peptide linking C6 H10 N3 O2 1 156.162 y HISTIDINE L-peptide linking C6 H13 N O2 131.173 y ISOLEUCINE L-peptide linking C6 H13 N O2 131.173 y LEUCINE L-peptide linking C6 H15 N2 O2 1 147.195 y LYSINE L-peptide linking C6 H13 N O2 131.173 n NORLEUCINE L-peptide linking C6 H14 N2 O 130.188 n L-leucinamide L-peptide linking C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking C5 H9 N O2 115.130 y PROLINE L-peptide linking C3 H7 N O3 105.093 y SERINE L-peptide linking C4 H9 N O3 119.119 y THREONINE L-peptide linking C11 H12 N2 O2 204.225 y TRYPTOPHAN L-peptide linking C9 H11 N O3 181.189 y TYROSINE L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking To Be Published 0353 Total synthesis and 3D structure determination of a highly hydrophobic antimicrobial Crassostrea gigas big defensin, enduring challenges rescue by a solubilizing tag 10.2210/pdb8bgk/pdb pdb_00008bgk 9977.422 Cg-BigDef5 MET14NLE 1 syn polymer no yes WAQALLPIWTYTQ(NLE)TVSAPLFAALVAAYGIYAVTRYGIKKARTRNDSHQCANNRGWCRKSCFGHEYIDWYYTDVCG SFYCCRPRN(NLW) WAQALLPIWTYTQLTVSAPLFAALVAAYGIYAVTRYGIKKARTRNDSHQCANNRGWCRKSCFGHEYIDWYYTDVCGSFYC CRPRNL B polypeptide(L) n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n repository Initial release 1 0 2022-12-07 France Agence Nationale de la Recherche (ANR) ANR-19-CE18-0025 karine.loth@cnrs-orleans.fr 0000-0001-7058-8661 Karine LOTH principal investigator/group leader NMR Structure of Big-defensin 5 from oyster Crassostrea gigas N PDBE Y PDBE 2022-10-27 REL REL REL 29159 Crassostrea gigas sample 1 86 N structures with the least restraint violations 200 10 isotropic 1 2D 1H-1H TOCSY isotropic 1 2D 1H-1H NOESY isotropic 1 2D 1H-15N HSQC isotropic 1 2D 1H-13C HSQC 1 mM natural abundance 0 mM conditions 4.7 pH 1 atm 298 K simulated annealing 1 closest to the average 1 mM Cg-BigDef5, 95% H2O/5% D2O unlabelled 95% H2O/5% D2O solution Bruker Biospin collection TopSpin Bruker Biospin processing TopSpin CCPN peak picking CcpNmr Analysis Linge, O'Donoghue and Nilges structure calculation ARIA 700 Bruker AVANCE III HD 700 TRP 1 n 1 TRP 1 B ALA 2 n 2 ALA 2 B GLN 3 n 3 GLN 3 B ALA 4 n 4 ALA 4 B LEU 5 n 5 LEU 5 B LEU 6 n 6 LEU 6 B PRO 7 n 7 PRO 7 B ILE 8 n 8 ILE 8 B TRP 9 n 9 TRP 9 B THR 10 n 10 THR 10 B TYR 11 n 11 TYR 11 B THR 12 n 12 THR 12 B GLN 13 n 13 GLN 13 B NLE 14 n 14 NLE 14 B THR 15 n 15 THR 15 B VAL 16 n 16 VAL 16 B SER 17 n 17 SER 17 B ALA 18 n 18 ALA 18 B PRO 19 n 19 PRO 19 B LEU 20 n 20 LEU 20 B PHE 21 n 21 PHE 21 B ALA 22 n 22 ALA 22 B ALA 23 n 23 ALA 23 B LEU 24 n 24 LEU 24 B VAL 25 n 25 VAL 25 B ALA 26 n 26 ALA 26 B ALA 27 n 27 ALA 27 B TYR 28 n 28 TYR 28 B GLY 29 n 29 GLY 29 B ILE 30 n 30 ILE 30 B TYR 31 n 31 TYR 31 B ALA 32 n 32 ALA 32 B VAL 33 n 33 VAL 33 B THR 34 n 34 THR 34 B ARG 35 n 35 ARG 35 B TYR 36 n 36 TYR 36 B GLY 37 n 37 GLY 37 B ILE 38 n 38 ILE 38 B LYS 39 n 39 LYS 39 B LYS 40 n 40 LYS 40 B ALA 41 n 41 ALA 41 B ARG 42 n 42 ARG 42 B THR 43 n 43 THR 43 B ARG 44 n 44 ARG 44 B ASN 45 n 45 ASN 45 B ASP 46 n 46 ASP 46 B SER 47 n 47 SER 47 B HIS 48 n 48 HIS 48 B GLN 49 n 49 GLN 49 B CYS 50 n 50 CYS 50 B ALA 51 n 51 ALA 51 B ASN 52 n 52 ASN 52 B ASN 53 n 53 ASN 53 B ARG 54 n 54 ARG 54 B GLY 55 n 55 GLY 55 B TRP 56 n 56 TRP 56 B CYS 57 n 57 CYS 57 B ARG 58 n 58 ARG 58 B LYS 59 n 59 LYS 59 B SER 60 n 60 SER 60 B CYS 61 n 61 CYS 61 B PHE 62 n 62 PHE 62 B GLY 63 n 63 GLY 63 B HIS 64 n 64 HIS 64 B GLU 65 n 65 GLU 65 B TYR 66 n 66 TYR 66 B ILE 67 n 67 ILE 67 B ASP 68 n 68 ASP 68 B TRP 69 n 69 TRP 69 B TYR 70 n 70 TYR 70 B TYR 71 n 71 TYR 71 B THR 72 n 72 THR 72 B ASP 73 n 73 ASP 73 B VAL 74 n 74 VAL 74 B CYS 75 n 75 CYS 75 B GLY 76 n 76 GLY 76 B SER 77 n 77 SER 77 B PHE 78 n 78 PHE 78 B TYR 79 n 79 TYR 79 B CYS 80 n 80 CYS 80 B CYS 81 n 81 CYS 81 B ARG 82 n 82 ARG 82 B PRO 83 n 83 PRO 83 B ARG 84 n 84 ARG 84 B ASN 85 n 85 ASN 85 B CLE 86 n 86 NLW 86 B author_defined_assembly 1 monomeric none 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 identity operation 0.0000000000 0.0000000000 0.0000000000 B N CYS 50 A N CYS 50 B O GLY 55 A O GLY 55 B N ARG 58 A N ARG 58 B O TYR 79 A O TYR 79 B O CYS 80 A O CYS 80 B N ASP 68 A N ASP 68 1 B B HH12 OE1 ARG GLU 58 65 1.60 2 B B O H TRP TYR 69 71 1.58 5 B B O H TRP TYR 69 71 1.58 7 B B O H TRP TYR 69 71 1.58 1 B ALA 2 61.85 -67.43 1 B ALA 4 -59.23 77.57 1 B LEU 5 -72.71 30.04 1 B LEU 6 -176.39 56.03 1 B ILE 8 -163.99 -97.75 1 B TRP 9 -56.41 -8.28 1 B TYR 11 -131.47 -84.01 1 B THR 12 -148.01 -83.24 1 B GLN 13 171.67 113.59 1 B VAL 16 -134.84 -82.88 1 B TYR 28 -107.55 -63.28 1 B ALA 41 58.97 87.19 1 B ARG 42 -178.80 -22.72 1 B THR 43 68.15 141.89 1 B ASN 45 -141.30 -159.63 1 B ASN 52 36.55 46.03 1 B ASN 53 -177.82 -38.52 1 B SER 60 178.90 145.37 1 B HIS 64 -169.55 24.93 1 B TRP 69 -117.34 -137.72 1 B TYR 70 69.56 -46.58 2 B ALA 4 -62.69 72.95 2 B ILE 8 -126.77 -93.37 2 B TRP 9 -56.34 0.36 2 B TYR 11 -110.46 -83.78 2 B THR 12 -141.85 -90.30 2 B GLN 13 179.15 -110.10 2 B NLE 14 69.63 174.84 2 B VAL 16 -128.77 -98.78 2 B TYR 28 -125.27 -68.08 2 B ILE 30 -178.40 -34.94 2 B THR 43 67.42 112.36 2 B ASN 52 39.88 27.48 2 B ASN 53 -164.38 -49.30 2 B SER 60 -179.76 149.25 2 B TRP 69 -100.09 -138.30 2 B TYR 70 67.88 -54.54 2 B ASN 85 -75.77 -145.81 3 B ALA 2 62.08 -60.48 3 B ALA 4 -55.75 90.22 3 B LEU 6 -164.21 61.71 3 B ILE 8 -161.24 -99.04 3 B TRP 9 -61.33 19.80 3 B THR 10 -149.86 -31.34 3 B TYR 11 -101.53 -83.71 3 B THR 12 -144.20 -106.09 3 B GLN 13 -167.42 73.63 3 B VAL 16 -137.38 -92.59 3 B TYR 28 -109.36 -65.19 3 B THR 43 70.14 134.74 3 B ARG 44 -80.83 -76.57 3 B ASN 53 -176.00 -38.50 3 B SER 60 179.50 142.56 3 B HIS 64 -161.27 23.80 3 B TRP 69 64.75 -40.70 3 B ASN 85 -79.68 -145.09 4 B LEU 5 -69.78 -149.15 4 B LEU 6 30.79 43.99 4 B ILE 8 -163.24 -104.41 4 B TYR 11 -104.82 -87.68 4 B THR 12 -143.06 -89.77 4 B GLN 13 175.86 67.05 4 B VAL 16 -135.92 -94.86 4 B ARG 42 -165.81 28.91 4 B THR 43 65.79 117.51 4 B ASN 45 66.65 162.16 4 B SER 47 -48.04 150.30 4 B ALA 51 69.55 -14.92 4 B ASN 53 -160.63 -41.41 4 B HIS 64 -159.95 26.25 4 B TRP 69 -101.96 -139.55 4 B TYR 70 66.19 -61.69 5 B ILE 8 -164.14 -89.15 5 B TYR 11 -114.55 -89.53 5 B THR 12 -149.59 -91.48 5 B GLN 13 -175.58 123.29 5 B VAL 16 -121.27 -112.01 5 B LYS 40 -103.52 58.98 5 B ALA 41 76.28 -10.72 5 B ALA 51 74.08 -12.34 5 B ASN 53 -164.42 -52.04 5 B SER 60 -175.42 146.39 5 B HIS 64 -166.85 22.16 5 B TRP 69 -102.45 -145.50 5 B TYR 70 61.32 -54.82 5 B CYS 80 -69.06 84.32 6 B ALA 4 -63.44 79.92 6 B ILE 8 -141.46 -90.90 6 B TRP 9 -61.27 10.99 6 B THR 10 -146.14 -22.68 6 B TYR 11 -106.06 -85.28 6 B THR 12 -133.46 -86.79 6 B GLN 13 -172.33 -68.75 6 B NLE 14 -76.98 -163.43 6 B THR 15 -33.21 125.86 6 B VAL 16 -138.72 -86.38 6 B ARG 42 -140.00 -89.29 6 B THR 43 -173.75 141.46 6 B ASN 45 173.64 153.61 6 B SER 47 -38.81 141.14 6 B ASN 52 36.24 37.41 6 B ASN 53 -173.79 -57.92 6 B SER 60 -177.29 139.40 6 B TRP 69 -113.25 -148.10 6 B TYR 70 56.94 -1.58 6 B TYR 71 -142.70 -27.99 6 B ASN 85 -74.76 -143.03 7 B LEU 5 -75.58 21.42 7 B LEU 6 -173.54 58.42 7 B PRO 7 -88.63 45.28 7 B ILE 8 -149.22 -101.16 7 B TRP 9 -61.82 15.78 7 B THR 10 -141.97 -25.11 7 B TYR 11 -105.88 -73.40 7 B THR 12 -154.60 -87.32 7 B GLN 13 166.72 89.02 7 B VAL 16 -140.69 -91.63 7 B ARG 42 -148.21 20.22 7 B THR 43 67.76 126.03 7 B ALA 51 69.32 -10.81 7 B ASN 53 -164.99 -40.37 7 B SER 60 -175.62 138.23 7 B HIS 64 -158.50 32.08 7 B TRP 69 -101.08 -144.37 7 B TYR 70 66.10 -56.34 8 B ALA 4 -62.06 86.96 8 B LEU 5 -75.96 22.16 8 B LEU 6 -159.75 44.49 8 B PRO 7 -89.23 40.22 8 B ILE 8 -154.58 -90.42 8 B TRP 9 -59.10 -0.81 8 B THR 10 -140.22 13.10 8 B TYR 11 -135.96 -88.32 8 B THR 12 -150.95 -83.25 8 B GLN 13 178.80 120.11 8 B VAL 16 -136.52 -93.64 8 B ALA 41 64.84 83.01 8 B ARG 42 -173.99 15.14 8 B ARG 44 55.40 -83.98 8 B ASN 45 -146.84 -154.65 8 B ASN 52 47.96 21.04 8 B ASN 53 -171.16 -49.84 8 B SER 60 -175.28 139.05 8 B HIS 64 -162.54 35.05 8 B TRP 69 49.57 -142.99 8 B TYR 70 68.59 -48.61 9 B ALA 2 -152.59 11.16 9 B GLN 3 -146.41 28.81 9 B ALA 4 30.03 67.92 9 B LEU 6 -154.00 45.98 9 B PRO 7 -85.93 36.49 9 B ILE 8 -149.85 -96.60 9 B TRP 9 -55.55 -8.45 9 B TYR 11 -88.57 -84.00 9 B THR 12 -148.37 -93.33 9 B GLN 13 -170.12 73.46 9 B VAL 16 -134.91 -96.61 9 B THR 43 65.55 142.71 9 B ARG 44 -59.21 -71.24 9 B ASN 45 -126.79 -156.91 9 B ALA 51 66.47 -3.48 9 B ASN 53 -179.40 -60.66 9 B SER 60 -177.48 129.23 9 B HIS 64 -98.06 30.75 9 B TRP 69 61.51 -35.90 10 B ALA 4 -64.49 83.24 10 B LEU 6 -142.46 40.55 10 B ILE 8 -127.15 -89.29 10 B TRP 9 -57.40 -8.58 10 B TYR 11 -102.24 -84.78 10 B THR 12 -144.88 -85.65 10 B GLN 13 -165.61 -84.64 10 B NLE 14 69.73 175.48 10 B VAL 16 -132.92 -96.71 10 B TYR 28 -107.05 -64.34 10 B ARG 42 -164.80 -93.98 10 B ASN 45 -150.74 -151.19 10 B ALA 51 72.41 -20.78 10 B ASN 53 -151.43 -30.88 10 B SER 60 -176.01 149.39 10 B HIS 64 -169.19 39.52 10 B TRP 69 -112.62 -139.90 10 B TYR 70 69.00 -55.28 N NMR Structure of Big-defensin 5 from oyster Crassostrea gigas 1 N N B SER 17 A SER 17 HELX_P B TYR 28 A TYR 28 1 AA1 12 B GLY 29 A GLY 29 HELX_P B GLY 37 A GLY 37 1 AA2 9 B TYR 71 A TYR 71 HELX_P B GLY 76 A GLY 76 1 AA3 6 disulf 2.154 B CYS 50 A SG CYS 50 1_555 B CYS 80 A SG CYS 80 1_555 disulf 2.173 B CYS 57 A SG CYS 57 1_555 B CYS 75 A SG CYS 75 1_555 disulf 2.228 B CYS 61 A SG CYS 61 1_555 B CYS 81 A SG CYS 81 1_555 covale 1.317 both B GLN 13 A C GLN 13 1_555 B NLE 14 A N NLE 14 1_555 covale 1.318 both B NLE 14 A C NLE 14 1_555 B THR 15 A N THR 15 1_555 covale 1.321 both B ASN 85 A C ASN 85 1_555 B NLW 86 A N NLW 86 1_555 ANTIMICROBIAL PROTEIN Antibacterial peptide, beta Defensin, Diversity, Evolution, Microbiome, Invertebrate, Mollusk, ANTIMICROBIAL PROTEIN 8BGK PDB 1 1 8BGK 1 86 8BGK 1 86 8BGK B 1 1 86 4 anti-parallel anti-parallel anti-parallel B HIS 48 A HIS 48 B CYS 50 A CYS 50 B GLY 55 A GLY 55 B ARG 58 A ARG 58 B TYR 79 A TYR 79 B PRO 83 A PRO 83 B GLU 65 A GLU 65 B ASP 68 A ASP 68