HEADER PLANT PROTEIN 29-APR-20 6WQL TITLE SOLUTION STRUCTURE OF THE SEED PEPTIDE C2 (VBP-1) FROM PUMPKIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: SEED PEPTIDE C2 (VBP-1); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: CUCURBITA MAXIMA; SOURCE 4 ORGANISM_COMMON: PUMPKIN; SOURCE 5 ORGANISM_TAXID: 3661 KEYWDS VICILIN-BURIED PEPTIDE, PLANT PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR C.P.PAYNE,K.J.ROSENGREN REVDAT 3 14-JUN-23 6WQL 1 REMARK REVDAT 2 04-NOV-20 6WQL 1 JRNL REVDAT 1 21-OCT-20 6WQL 0 JRNL AUTH C.D.PAYNE,G.VADLAMANI,M.F.FISHER,J.ZHANG,R.J.CLARK, JRNL AUTH 2 J.S.MYLNE,K.J.ROSENGREN JRNL TITL DEFINING THE FAMILIAL FOLD OF THE VICILIN-BURIED PEPTIDE JRNL TITL 2 FAMILY. JRNL REF J.NAT.PROD. V. 83 3030 2020 JRNL REFN ESSN 1520-6025 JRNL PMID 32997497 JRNL DOI 10.1021/ACS.JNATPROD.0C00594 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: CYANA FOR INITIAL CALCULATIONS FOR REMARK 3 INTER-PROTON DISTANCE RESTRAINTS, CNS FOR REFINEMENT IN EXPLICIT REMARK 3 WATER REMARK 4 REMARK 4 6WQL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-APR-20. REMARK 100 THE DEPOSITION ID IS D_1000248719. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 3.5 REMARK 210 IONIC STRENGTH : 0 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 2 MG/ML C2, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H TOCSY; 2D 1H-1H NOESY; REMARK 210 2D 1H-13C HSQC; 2D 1H-15N 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, CARA, CYANA 3.97, CNS REMARK 210 1.2 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 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: 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 VAL A 48 89.89 72.84 REMARK 500 2 ARG A 2 -84.65 66.54 REMARK 500 2 GLU A 20 94.26 67.20 REMARK 500 2 ASP A 47 78.93 52.83 REMARK 500 3 GLU A 46 -73.75 60.96 REMARK 500 5 VAL A 48 91.43 64.48 REMARK 500 6 GLU A 46 102.79 -160.63 REMARK 500 8 SER A 4 109.69 -54.13 REMARK 500 8 ARG A 44 93.18 64.93 REMARK 500 9 GLU A 20 88.29 71.04 REMARK 500 11 GLU A 20 142.43 -175.47 REMARK 500 11 ARG A 44 105.56 -51.56 REMARK 500 13 ARG A 2 80.47 62.98 REMARK 500 16 VAL A 48 93.91 -68.36 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 13 ARG A 36 0.07 SIDE CHAIN REMARK 500 19 ARG A 36 0.08 SIDE CHAIN REMARK 500 20 ARG A 36 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6WQJ RELATED DB: PDB REMARK 900 RELATED VICILIN-BURIED PEPTIDE DESCRIBED IN THE SAME PUBLICATION. REMARK 900 RELATED ID: 30749 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF THE SEED PEPTIDE C2 (VBP-1) FROM PUMPKIN DBREF 6WQL A 2 49 UNP Q9ZWI3 Q9ZWI3_CUCMA 71 118 SEQADV 6WQL PCA A 1 UNP Q9ZWI3 EXPRESSION TAG SEQRES 1 A 49 PCA ARG GLY SER PRO ARG ALA GLU TYR GLU VAL CYS ARG SEQRES 2 A 49 LEU ARG CYS GLN VAL ALA GLU ARG GLY VAL GLU GLN GLN SEQRES 3 A 49 ARG LYS CYS GLU GLN VAL CYS GLU GLU ARG LEU ARG GLU SEQRES 4 A 49 ARG GLU GLN GLY ARG GLY GLU ASP VAL ASP HET PCA A 1 14 HETNAM PCA PYROGLUTAMIC ACID FORMUL 1 PCA C5 H7 N O3 HELIX 1 AA1 SER A 4 ALA A 19 1 16 HELIX 2 AA2 GLY A 22 GLN A 42 1 21 SSBOND 1 CYS A 12 CYS A 33 1555 1555 2.03 SSBOND 2 CYS A 16 CYS A 29 1555 1555 2.01 LINK C PCA A 1 N ARG A 2 1555 1555 1.31 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 -15.545 5.063 -6.202 1.00 0.00 N HETATM 2 CA PCA A 1 -14.928 5.822 -5.124 1.00 0.00 C HETATM 3 CB PCA A 1 -15.648 5.411 -3.852 1.00 0.00 C HETATM 4 CG PCA A 1 -16.847 4.594 -4.292 1.00 0.00 C HETATM 5 CD PCA A 1 -16.706 4.543 -5.807 1.00 0.00 C HETATM 6 OE PCA A 1 -17.575 4.077 -6.553 1.00 0.00 O HETATM 7 C PCA A 1 -13.444 5.504 -5.024 1.00 0.00 C HETATM 8 O PCA A 1 -12.914 4.734 -5.839 1.00 0.00 O HETATM 9 H PCA A 1 -15.130 4.951 -7.083 1.00 0.00 H HETATM 10 HA PCA A 1 -15.038 6.882 -5.301 1.00 0.00 H HETATM 11 HB2 PCA A 1 -15.971 6.291 -3.297 1.00 0.00 H HETATM 12 HB3 PCA A 1 -14.987 4.801 -3.236 1.00 0.00 H HETATM 13 HG2 PCA A 1 -17.780 5.096 -4.041 1.00 0.00 H HETATM 14 HG3 PCA A 1 -16.807 3.596 -3.856 1.00 0.00 H