HEADER PLANT PROTEIN 27-FEB-19 6O3Q TITLE NMR SOLUTION STRUCTURE OF VICILIN-BURIED PEPTIDE-8 (VBP-8) COMPND MOL_ID: 1; COMPND 2 MOLECULE: VICILIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SOLANUM LYCOPERSICUM; SOURCE 4 ORGANISM_COMMON: TOMATO; SOURCE 5 ORGANISM_TAXID: 4081 KEYWDS SEED PEPTIDE, PLANT PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR K.J.ROSENGREN,C.PAYNE REVDAT 4 14-JUN-23 6O3Q 1 REMARK REVDAT 3 01-JAN-20 6O3Q 1 REMARK REVDAT 2 29-MAY-19 6O3Q 1 JRNL REMARK REVDAT 1 24-APR-19 6O3Q 0 JRNL AUTH J.ZHANG,C.D.PAYNE,B.POUVREAU,H.SCHAEFER,M.F.FISHER, JRNL AUTH 2 N.L.TAYLOR,O.BERKOWITZ,J.WHELAN,K.J.ROSENGREN,J.S.MYLNE JRNL TITL AN ANCIENT PEPTIDE FAMILY BURIED WITHIN VICILIN PRECURSORS. JRNL REF ACS CHEM.BIOL. V. 14 979 2019 JRNL REFN ESSN 1554-8937 JRNL PMID 30973714 JRNL DOI 10.1021/ACSCHEMBIO.9B00167 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: CALCULATED USING TORSION AND DYNAMICS REMARK 3 THEN REFINED AND ENERGY MINIMISED IN EXPLICIT SOLVENT. REMARK 4 REMARK 4 6O3Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-MAR-19. REMARK 100 THE DEPOSITION ID IS D_1000239950. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 288; 293; 303; 308 REMARK 210 PH : 4; 4; 4; 4; 4 REMARK 210 IONIC STRENGTH : 0; 0; 0; 0; 0 REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT; REMARK 210 AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 2 MG/ML VBP-8, 90% 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 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN 4, CARA, CYANA 3.9 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE REMARK 210 COVALENT GEOMETRY 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: 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 HZ3 LYS A 5 OE1 GLU A 47 1.58 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 43 109.93 -57.05 REMARK 500 3 THR A 48 -44.64 -145.14 REMARK 500 10 HIS A 44 118.15 -160.86 REMARK 500 11 GLU A 47 74.29 -100.87 REMARK 500 12 HIS A 44 -57.54 73.34 REMARK 500 15 PRO A 3 174.33 -59.31 REMARK 500 18 THR A 48 21.73 -149.55 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 15 ARG A 1 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30579 RELATED DB: BMRB REMARK 900 NMR SOLUTION STRUCTURE OF VICILIN-BURIED PEPTIDE-8 (VBP-8) DBREF 6O3Q A 1 49 UNP B0JEU3 B0JEU3_SOLLC 87 135 SEQRES 1 A 49 ARG GLY PRO ASP LYS SER TYR LYS ARG LEU GLN GLU CYS SEQRES 2 A 49 GLN ARG ARG CYS GLN SER GLU GLN GLN GLY GLN ARG LEU SEQRES 3 A 49 GLN GLU CYS GLN GLN ARG CYS GLN GLN GLU TYR GLN ARG SEQRES 4 A 49 GLU LYS GLY GLN HIS GLN GLY GLU THR ASN HELIX 1 AA1 ASP A 4 GLN A 21 1 18 HELIX 2 AA2 GLN A 22 GLY A 42 1 21 SSBOND 1 CYS A 13 CYS A 33 1555 1555 2.02 SSBOND 2 CYS A 17 CYS A 29 1555 1555 2.03 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