HEADER ANTIMICROBIAL PROTEIN 21-DEC-18 6QBL TITLE NMR STRUCTURE OF BIG-DEFENSIN 1 FROM OYSTER CRASSOSTREA GIGAS COMPND MOL_ID: 1; COMPND 2 MOLECULE: BIG DEFENSIN 1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: CRASSOSTREA GIGAS; SOURCE 4 ORGANISM_COMMON: PACIFIC OYSTER; SOURCE 5 ORGANISM_TAXID: 29159 KEYWDS BIG-DEFENSIN, ANTIMICROBIAL, MARINE, OYSTER, SALT INSENSITIVE KEYWDS 2 ACTIVITY, ANTIMICROBIAL PROTEIN EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR K.LOTH,H.MEUDAL,A.F.DELMAS REVDAT 1 11-DEC-19 6QBL 0 JRNL AUTH K.LOTH,A.VERGNES,C.BARRETO,S.N.VOISIN,H.MEUDAL,J.DA SILVA, JRNL AUTH 2 A.BRESSAN,N.BELMADI,E.BACHERE,V.AUCAGNE,C.CAZEVIELLE, JRNL AUTH 3 H.MARCHANDIN,R.D.ROSA,P.BULET,L.TOUQUI,A.F.DELMAS, JRNL AUTH 4 D.DESTOUMIEUX-GARZON JRNL TITL THE ANCESTRAL N-TERMINAL DOMAIN OF BIG DEFENSINS DRIVES JRNL TITL 2 BACTERIALLY TRIGGERED ASSEMBLY INTO ANTIMICROBIAL NANONETS. JRNL REF MBIO V. 10 2019 JRNL REFN ESSN 2150-7511 JRNL PMID 31641083 JRNL DOI 10.1128/MBIO.01821-19 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6QBL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-DEC-18. REMARK 100 THE DEPOSITION ID IS D_1200013509. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 4.6 REMARK 210 IONIC STRENGTH : 0 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1.0 MM [1-93]CG-BIGDEF1, 90% REMARK 210 H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H TOCSY; 2D 1H-1H NOESY; REMARK 210 2D 1H-15N HSQC; 2D 1H-13C HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III HD REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : ARIA, CCPNMR ANALYSIS REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 150 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : TOTAL ENERGIES AND RESTRAINT REMARK 210 VIOLATION STATISTICS 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5530 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE 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 GLN A 3 125.97 -176.11 REMARK 500 1 ALA A 4 70.24 55.00 REMARK 500 1 LEU A 5 -157.52 -94.65 REMARK 500 1 ALA A 12 105.60 -58.61 REMARK 500 1 ARG A 49 49.46 -84.87 REMARK 500 1 SER A 50 -161.93 57.91 REMARK 500 1 ASP A 51 -83.45 -162.94 REMARK 500 1 HIS A 52 -77.54 -140.90 REMARK 500 1 HIS A 71 -9.86 158.12 REMARK 500 1 ARG A 92 38.26 -165.95 REMARK 500 2 ALA A 2 -124.88 57.67 REMARK 500 2 GLN A 3 127.35 -37.27 REMARK 500 2 ALA A 4 64.06 86.54 REMARK 500 2 ASN A 43 77.94 -159.26 REMARK 500 2 ARG A 47 43.67 -89.56 REMARK 500 2 ARG A 49 56.80 -93.96 REMARK 500 2 SER A 50 -172.22 58.40 REMARK 500 2 ASP A 51 -74.27 -158.67 REMARK 500 2 HIS A 52 -70.04 -150.05 REMARK 500 2 SER A 70 88.19 -68.73 REMARK 500 2 HIS A 71 -8.89 156.05 REMARK 500 2 ARG A 92 41.07 -174.57 REMARK 500 3 ALA A 2 169.79 66.67 REMARK 500 3 ALA A 4 71.39 174.42 REMARK 500 3 LEU A 5 -167.18 -105.85 REMARK 500 3 ALA A 12 108.40 -57.84 REMARK 500 3 ASN A 43 33.10 -143.65 REMARK 500 3 TYR A 45 -169.86 -113.35 REMARK 500 3 SER A 50 120.06 59.80 REMARK 500 3 HIS A 71 -6.56 152.78 REMARK 500 3 ARG A 92 -40.30 -154.07 REMARK 500 4 ALA A 2 -164.76 63.32 REMARK 500 4 GLN A 3 123.61 67.40 REMARK 500 4 ALA A 4 77.90 57.12 REMARK 500 4 LEU A 5 -162.15 -106.51 REMARK 500 4 ASN A 43 137.68 79.75 REMARK 500 4 ARG A 47 48.81 -150.94 REMARK 500 4 ARG A 49 49.83 -83.51 REMARK 500 4 SER A 50 -159.50 58.99 REMARK 500 4 ASP A 51 -154.31 -174.13 REMARK 500 4 HIS A 71 -7.23 158.78 REMARK 500 4 ARG A 92 40.73 -167.60 REMARK 500 5 ALA A 4 71.01 55.01 REMARK 500 5 PRO A 7 150.49 -48.03 REMARK 500 5 SER A 50 170.13 172.03 REMARK 500 5 ASP A 51 -74.09 171.40 REMARK 500 5 HIS A 52 -72.10 -167.53 REMARK 500 5 HIS A 71 -8.09 157.19 REMARK 500 5 ARG A 92 30.58 -158.90 REMARK 500 6 ALA A 2 139.50 69.97 REMARK 500 REMARK 500 THIS ENTRY HAS 98 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34346 RELATED DB: BMRB REMARK 900 NMR STRUCTURE OF BIG-DEFENSIN 1 FROM OYSTER CRASSOSTREA GIGAS DBREF 6QBL A 1 93 UNP F6M2J2 F6M2J2_CRAGI 37 129 SEQRES 1 A 93 PCA ALA GLN ALA LEU LEU PRO ILE ALA SER TYR ALA GLY SEQRES 2 A 93 LEU THR VAL SER ALA PRO VAL PHE ALA ALA LEU VAL THR SEQRES 3 A 93 VAL TYR GLY ALA TYR ALA LEU TYR ARG TYR ASN ILE ARG SEQRES 4 A 93 ARG ARG GLU ASN SER TYR GLN ARG ILE ARG SER ASP HIS SEQRES 5 A 93 ASP SER HIS SER CYS ALA ASN ASN ARG GLY TRP CYS ARG SEQRES 6 A 93 PRO THR CYS PHE SER HIS GLU TYR THR ASP TRP PHE ASN SEQRES 7 A 93 ASN ASP VAL CYS GLY SER TYR ARG CYS CYS ARG PRO GLY SEQRES 8 A 93 ARG AAR MODRES 6QBL PCA A 1 GLN MODIFIED RESIDUE MODRES 6QBL AAR A 93 ARG MODIFIED RESIDUE HET PCA A 1 14 HET AAR A 93 27 HETNAM PCA PYROGLUTAMIC ACID HETNAM AAR ARGININEAMIDE FORMUL 1 PCA C5 H7 N O3 FORMUL 1 AAR C6 H16 N5 O 1+ HELIX 1 AA1 SER A 17 TYR A 28 1 12 HELIX 2 AA2 TYR A 28 TYR A 36 1 9 HELIX 3 AA3 TRP A 76 GLY A 83 1 8 SHEET 1 AA1 2 THR A 15 VAL A 16 0 SHEET 2 AA1 2 ARG A 39 ARG A 40 1 O ARG A 39 N VAL A 16 SHEET 1 AA2 4 SER A 56 CYS A 57 0 SHEET 2 AA2 4 GLY A 62 ARG A 65 -1 O GLY A 62 N CYS A 57 SHEET 3 AA2 4 ARG A 86 GLY A 91 -1 O CYS A 88 N TRP A 63 SHEET 4 AA2 4 HIS A 71 ASP A 75 -1 N ASP A 75 O CYS A 87 SSBOND 1 CYS A 57 CYS A 87 1555 1555 2.20 SSBOND 2 CYS A 64 CYS A 82 1555 1555 2.15 SSBOND 3 CYS A 68 CYS A 88 1555 1555 2.23 LINK C PCA A 1 N ALA A 2 1555 1555 1.34 LINK C ARG A 92 N AAR A 93 1555 1555 1.33 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 MODEL 1 HETATM 1 N PCA A 1 0.917 -3.194 11.149 1.00 0.00 N HETATM 2 CA PCA A 1 0.985 -2.720 9.756 1.00 0.00 C HETATM 3 CB PCA A 1 -0.274 -1.902 9.450 1.00 0.00 C HETATM 4 CG PCA A 1 -1.031 -1.891 10.745 1.00 0.00 C HETATM 5 CD PCA A 1 -0.123 -2.621 11.715 1.00 0.00 C HETATM 6 OE PCA A 1 -0.153 -2.355 12.920 1.00 0.00 O HETATM 7 C PCA A 1 2.232 -1.873 9.555 1.00 0.00 C HETATM 8 O PCA A 1 2.854 -1.455 10.531 1.00 0.00 O HETATM 9 H PCA A 1 1.794 -2.972 11.568 1.00 0.00 H HETATM 10 HA PCA A 1 1.027 -3.576 9.101 1.00 0.00 H HETATM 11 HB2 PCA A 1 0.007 -0.905 9.143 1.00 0.00 H HETATM 12 HB3 PCA A 1 -0.840 -2.382 8.666 1.00 0.00 H HETATM 13 HG2 PCA A 1 -1.194 -0.875 11.082 1.00 0.00 H HETATM 14 HG3 PCA A 1 -1.959 -2.431 10.653 1.00 0.00 H