PDB Short entry for 1AYJ HEADER FUNGICIDE 05-NOV-97 1AYJ TITLE DETERMINATION OF THE THREE-DIMENSIONAL SOLUTION STRUCTURE OF RAPHANUS TITLE 2 SATIVUS ANTIFUNGAL PROTEIN 1 (RS-AFP1) BY 1H NMR, 20 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANTIFUNGAL PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RS-AFP1 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RAPHANUS SATIVUS VAR. NIGER; SOURCE 3 ORGANISM_COMMON: CHINESE RADISH; SOURCE 4 ORGANISM_TAXID: 41679; SOURCE 5 STRAIN: VAR. NIGER; SOURCE 6 ORGAN: SEED KEYWDS FUNGICIDE, PLANT DEFENSIN, CYSTEINE-STABILIZED ALFA/BETA MOTIF EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR F.FANT,F.A.M.BORREMANS REVDAT 4 25-DEC-19 1AYJ 1 REMARK SEQRES LINK REVDAT 3 29-NOV-17 1AYJ 1 REMARK HELIX REVDAT 2 24-FEB-09 1AYJ 1 VERSN REVDAT 1 28-JAN-98 1AYJ 0 JRNL AUTH F.FANT,W.VRANKEN,W.BROEKAERT,F.BORREMANS JRNL TITL DETERMINATION OF THE THREE-DIMENSIONAL SOLUTION STRUCTURE OF JRNL TITL 2 RAPHANUS SATIVUS ANTIFUNGAL PROTEIN 1 BY 1H NMR. JRNL REF J.MOL.BIOL. V. 279 257 1998 JRNL REFN ISSN 0022-2836 JRNL PMID 9636715 JRNL DOI 10.1006/JMBI.1998.1767 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH F.FANT,W.F.VRANKEN,J.C.MARTINS,F.A.M.BORREMANS REMARK 1 TITL SOLUTION CONFORMATION OF RAPHANUS SATIVUS ANTIFUNGAL PROTEIN REMARK 1 TITL 2 1 (RS-AFP1) BY 1H NUCLEAR MAGNETIC RESONANCE. RESONANCE REMARK 1 TITL 3 ASSIGNMENTS, SECONDARY STRUCTURE AND GLOBAL FOLD REMARK 1 REF BULL.SOC.CHIM.BELG. V. 106 51 1997 REMARK 1 REFN ISSN 0037-9646 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : MSI/BIOSYM TECHNOLOGIES REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: SIMULATED ANNEALING PROTOCOL ADOPTED REMARK 3 NILGES ET AL. 1988, FEBS LETTERS, VOL. 239, PP129-136. INSIGHT REMARK 3 II ALSO WAS USED. REMARK 4 REMARK 4 1AYJ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000171412. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 305 REMARK 210 PH : 4.2 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : DQF-COSY; E.COSY; NOESY; TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : AM500 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : DIANA/REDAC, INSIGHTII/DISCOVER REMARK 210 METHOD USED : DIANA AND SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 500 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : LEAST RESTRAINT VIOLATION AND REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL 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 GLU A 5 CD GLU A 5 OE2 0.108 REMARK 500 1 GLU A 29 CD GLU A 29 OE2 0.105 REMARK 500 1 CYS A 51 C CYS A 51 OXT 0.133 REMARK 500 2 GLU A 5 CD GLU A 5 OE2 0.106 REMARK 500 2 GLU A 29 CD GLU A 29 OE2 0.108 REMARK 500 2 CYS A 51 C CYS A 51 OXT 0.133 REMARK 500 3 GLU A 5 CD GLU A 5 OE2 0.108 REMARK 500 3 GLU A 29 CD GLU A 29 OE2 0.107 REMARK 500 3 CYS A 51 C CYS A 51 OXT 0.132 REMARK 500 4 GLU A 5 CD GLU A 5 OE2 0.108 REMARK 500 4 GLU A 29 CD GLU A 29 OE2 0.108 REMARK 500 4 CYS A 51 C CYS A 51 OXT 0.131 REMARK 500 5 GLU A 5 CD GLU A 5 OE2 0.107 REMARK 500 5 GLU A 29 CD GLU A 29 OE2 0.106 REMARK 500 5 CYS A 51 C CYS A 51 OXT 0.133 REMARK 500 6 GLU A 5 CD GLU A 5 OE2 0.108 REMARK 500 6 GLU A 29 CD GLU A 29 OE2 0.105 REMARK 500 6 CYS A 51 C CYS A 51 OXT 0.132 REMARK 500 7 GLU A 5 CD GLU A 5 OE2 0.111 REMARK 500 7 GLU A 29 CD GLU A 29 OE2 0.115 REMARK 500 7 CYS A 51 C CYS A 51 OXT 0.132 REMARK 500 8 GLU A 5 CD GLU A 5 OE2 0.108 REMARK 500 8 GLU A 29 CD GLU A 29 OE2 0.106 REMARK 500 8 CYS A 51 C CYS A 51 OXT 0.133 REMARK 500 9 GLU A 5 CD GLU A 5 OE2 0.106 REMARK 500 9 GLU A 29 CD GLU A 29 OE2 0.109 REMARK 500 9 CYS A 51 C CYS A 51 OXT 0.132 REMARK 500 10 GLU A 5 CD GLU A 5 OE2 0.107 REMARK 500 10 GLU A 29 CD GLU A 29 OE2 0.108 REMARK 500 10 CYS A 51 C CYS A 51 OXT 0.132 REMARK 500 11 GLU A 5 CD GLU A 5 OE2 0.108 REMARK 500 11 GLU A 29 CD GLU A 29 OE2 0.108 REMARK 500 11 CYS A 51 C CYS A 51 OXT 0.132 REMARK 500 12 GLU A 5 CD GLU A 5 OE2 0.109 REMARK 500 12 GLU A 29 CD GLU A 29 OE2 0.109 REMARK 500 12 CYS A 51 C CYS A 51 OXT 0.133 REMARK 500 13 GLU A 5 CD GLU A 5 OE2 0.107 REMARK 500 13 GLU A 29 CD GLU A 29 OE2 0.105 REMARK 500 13 CYS A 51 C CYS A 51 OXT 0.132 REMARK 500 14 GLU A 5 CD GLU A 5 OE2 0.108 REMARK 500 14 GLU A 29 CD GLU A 29 OE2 0.111 REMARK 500 14 CYS A 51 C CYS A 51 OXT 0.132 REMARK 500 15 GLU A 5 CD GLU A 5 OE2 0.108 REMARK 500 15 GLU A 29 CD GLU A 29 OE2 0.107 REMARK 500 15 CYS A 51 C CYS A 51 OXT 0.131 REMARK 500 16 GLU A 5 CD GLU A 5 OE2 0.107 REMARK 500 16 GLU A 29 CD GLU A 29 OE2 0.109 REMARK 500 16 CYS A 51 C CYS A 51 OXT 0.133 REMARK 500 17 GLU A 5 CD GLU A 5 OE2 0.108 REMARK 500 17 GLU A 29 CD GLU A 29 OE2 0.107 REMARK 500 REMARK 500 THIS ENTRY HAS 60 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 THR A 10 -72.53 -84.10 REMARK 500 1 ASN A 17 107.57 -168.21 REMARK 500 1 LEU A 28 -71.61 -75.01 REMARK 500 1 ALA A 31 165.30 -43.52 REMARK 500 1 ARG A 32 -74.54 -86.86 REMARK 500 1 TYR A 38 -123.57 -83.22 REMARK 500 1 VAL A 39 154.25 69.24 REMARK 500 2 THR A 10 -68.23 -109.71 REMARK 500 2 TRP A 11 73.47 -64.79 REMARK 500 2 ASN A 17 136.75 -170.79 REMARK 500 2 ALA A 31 156.16 -44.79 REMARK 500 2 TYR A 38 -123.56 -82.02 REMARK 500 2 VAL A 39 153.07 68.87 REMARK 500 3 THR A 10 -70.38 -142.16 REMARK 500 3 TRP A 11 81.43 -68.85 REMARK 500 3 ASN A 17 134.25 -170.81 REMARK 500 3 ALA A 31 156.63 -38.98 REMARK 500 3 ALA A 42 81.56 -172.68 REMARK 500 3 HIS A 43 117.24 87.97 REMARK 500 4 LEU A 28 -76.24 -69.96 REMARK 500 4 ALA A 31 -164.79 -48.53 REMARK 500 4 ARG A 32 -53.72 -132.35 REMARK 500 4 ALA A 42 65.68 -163.60 REMARK 500 4 HIS A 43 135.43 92.71 REMARK 500 5 ASN A 17 132.56 -171.71 REMARK 500 5 LEU A 28 -70.14 -71.46 REMARK 500 5 ALA A 31 160.30 -44.66 REMARK 500 5 ARG A 32 -78.80 -83.50 REMARK 500 6 PRO A 7 -77.75 -73.20 REMARK 500 6 THR A 10 -96.31 -86.09 REMARK 500 6 TRP A 11 91.91 -68.32 REMARK 500 6 SER A 12 63.96 -105.15 REMARK 500 6 CYS A 15 -56.11 -120.32 REMARK 500 6 ASN A 17 106.83 -165.62 REMARK 500 6 ALA A 31 163.77 -47.08 REMARK 500 6 ARG A 32 -72.89 -88.00 REMARK 500 6 HIS A 43 154.48 75.97 REMARK 500 7 PRO A 7 -160.98 -76.95 REMARK 500 7 SER A 8 83.29 -59.54 REMARK 500 7 THR A 10 -58.31 -156.21 REMARK 500 7 ALA A 31 161.31 -42.28 REMARK 500 7 ARG A 32 -76.61 -82.75 REMARK 500 7 SER A 35 100.48 -178.31 REMARK 500 7 PHE A 40 150.09 -41.41 REMARK 500 8 SER A 8 -69.41 -24.65 REMARK 500 8 THR A 10 -72.60 -83.74 REMARK 500 8 TRP A 11 77.32 -65.63 REMARK 500 8 ASN A 17 131.47 -172.35 REMARK 500 8 SER A 35 133.23 -171.56 REMARK 500 8 ALA A 42 55.93 -161.00 REMARK 500 REMARK 500 THIS ENTRY HAS 119 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 TYR A 38 0.17 SIDE CHAIN REMARK 500 2 ARG A 32 0.12 SIDE CHAIN REMARK 500 2 TYR A 38 0.17 SIDE CHAIN REMARK 500 2 TYR A 48 0.07 SIDE CHAIN REMARK 500 3 ARG A 6 0.10 SIDE CHAIN REMARK 500 3 ARG A 32 0.09 SIDE CHAIN REMARK 500 3 TYR A 38 0.10 SIDE CHAIN REMARK 500 3 PHE A 49 0.09 SIDE CHAIN REMARK 500 4 TYR A 38 0.15 SIDE CHAIN REMARK 500 5 ARG A 32 0.08 SIDE CHAIN REMARK 500 5 TYR A 38 0.14 SIDE CHAIN REMARK 500 6 TYR A 38 0.15 SIDE CHAIN REMARK 500 6 PHE A 49 0.10 SIDE CHAIN REMARK 500 7 TYR A 38 0.11 SIDE CHAIN REMARK 500 7 TYR A 48 0.08 SIDE CHAIN REMARK 500 8 ARG A 6 0.20 SIDE CHAIN REMARK 500 8 ARG A 32 0.09 SIDE CHAIN REMARK 500 8 TYR A 38 0.18 SIDE CHAIN REMARK 500 8 PHE A 49 0.13 SIDE CHAIN REMARK 500 9 TYR A 38 0.09 SIDE CHAIN REMARK 500 9 PHE A 49 0.13 SIDE CHAIN REMARK 500 10 ARG A 32 0.08 SIDE CHAIN REMARK 500 10 TYR A 38 0.17 SIDE CHAIN REMARK 500 10 TYR A 48 0.07 SIDE CHAIN REMARK 500 11 ARG A 32 0.08 SIDE CHAIN REMARK 500 11 TYR A 38 0.13 SIDE CHAIN REMARK 500 11 TYR A 48 0.07 SIDE CHAIN REMARK 500 12 TYR A 38 0.15 SIDE CHAIN REMARK 500 14 ARG A 32 0.09 SIDE CHAIN REMARK 500 14 TYR A 38 0.16 SIDE CHAIN REMARK 500 14 TYR A 48 0.07 SIDE CHAIN REMARK 500 15 ARG A 32 0.10 SIDE CHAIN REMARK 500 15 TYR A 38 0.18 SIDE CHAIN REMARK 500 16 TYR A 38 0.09 SIDE CHAIN REMARK 500 17 ARG A 32 0.11 SIDE CHAIN REMARK 500 17 TYR A 38 0.16 SIDE CHAIN REMARK 500 17 TYR A 48 0.08 SIDE CHAIN REMARK 500 18 ARG A 32 0.10 SIDE CHAIN REMARK 500 18 TYR A 38 0.16 SIDE CHAIN REMARK 500 18 PHE A 49 0.09 SIDE CHAIN REMARK 500 19 ARG A 32 0.11 SIDE CHAIN REMARK 500 19 TYR A 38 0.17 SIDE CHAIN REMARK 500 20 TYR A 38 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1AYJ A 2 51 UNP P30231 AFP1_SINAL 2 51 SEQRES 1 A 51 PCA LYS LEU CYS GLU ARG PRO SER GLY THR TRP SER GLY SEQRES 2 A 51 VAL CYS GLY ASN ASN ASN ALA CYS LYS ASN GLN CYS ILE SEQRES 3 A 51 ASN LEU GLU LYS ALA ARG HIS GLY SER CYS ASN TYR VAL SEQRES 4 A 51 PHE PRO ALA HIS LYS CYS ILE CYS TYR PHE PRO CYS MODRES 1AYJ PCA A 1 GLN PYROGLUTAMIC ACID HET PCA A 1 14 HETNAM PCA PYROGLUTAMIC ACID FORMUL 1 PCA C5 H7 N O3 HELIX 1 1 ASN A 18 LEU A 28 1 11 SHEET 1 A 3 CYS A 4 PRO A 7 0 SHEET 2 A 3 LYS A 44 PHE A 49 -1 N PHE A 49 O CYS A 4 SHEET 3 A 3 HIS A 33 ASN A 37 -1 N ASN A 37 O LYS A 44 SSBOND 1 CYS A 4 CYS A 51 1555 1555 2.07 SSBOND 2 CYS A 15 CYS A 36 1555 1555 2.07 SSBOND 3 CYS A 21 CYS A 45 1555 1555 2.08 SSBOND 4 CYS A 25 CYS A 47 1555 1555 2.07 LINK C PCA A 1 N LYS A 2 1555 1555 1.34 CISPEP 1 PHE A 40 PRO A 41 1 -9.98 CISPEP 2 PHE A 40 PRO A 41 2 -10.39 CISPEP 3 PHE A 40 PRO A 41 3 0.80 CISPEP 4 PHE A 40 PRO A 41 4 -8.96 CISPEP 5 PHE A 40 PRO A 41 5 -10.45 CISPEP 6 PHE A 40 PRO A 41 6 -8.23 CISPEP 7 PHE A 40 PRO A 41 7 -5.78 CISPEP 8 PHE A 40 PRO A 41 8 -10.34 CISPEP 9 PHE A 40 PRO A 41 9 -10.59 CISPEP 10 PHE A 40 PRO A 41 10 -10.80 CISPEP 11 PHE A 40 PRO A 41 11 -10.34 CISPEP 12 PHE A 40 PRO A 41 12 -10.71 CISPEP 13 PHE A 40 PRO A 41 13 -10.37 CISPEP 14 PHE A 40 PRO A 41 14 -10.22 CISPEP 15 PHE A 40 PRO A 41 15 -10.65 CISPEP 16 PHE A 40 PRO A 41 16 6.06 CISPEP 17 PHE A 40 PRO A 41 17 -10.70 CISPEP 18 PHE A 40 PRO A 41 18 -10.66 CISPEP 19 PHE A 40 PRO A 41 19 -10.66 CISPEP 20 PHE A 40 PRO A 41 20 6.88 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