HEADER PLANT PROTEIN 17-NOV-99 1DF6 TITLE 1H NMR SOLUTION STRUCTURE OF CYCLOVIOLACIN O1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYCLOVIOLACIN O1; COMPND 3 CHAIN: A; COMPND 4 OTHER_DETAILS: CYCLIC CYSTINE KNOT POLYPEPTIDE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIOLA ODORATA; SOURCE 3 ORGANISM_TAXID: 97441; SOURCE 4 OTHER_DETAILS: LEAVES, STEMS AND FLOWERS KEYWDS CYCLIC CYSTINE KNOT, BACKBONE CYCLIC, 3-10 HELIX, DOUBLE-STRANDED KEYWDS 2 ANTI- PARALLEL BETA-SHEET, HAIRPIN BENDS, LOOPS, PLANT PROTEIN EXPDTA SOLUTION NMR NUMMDL 16 AUTHOR D.J.CRAIK,N.L.DALY,T.BOND,C.WAINE REVDAT 4 13-NOV-24 1DF6 1 REMARK REVDAT 3 16-FEB-22 1DF6 1 REMARK LINK REVDAT 2 24-FEB-09 1DF6 1 VERSN REVDAT 1 01-MAR-00 1DF6 0 JRNL AUTH D.J.CRAIK,N.L.DALY,T.BOND,C.WAINE JRNL TITL PLANT CYCLOTIDES: A UNIQUE FAMILY OF CYCLIC AND KNOTTED JRNL TITL 2 PROTEINS THAT DEFINES THE CYCLIC CYSTINE KNOT STRUCTURAL JRNL TITL 3 MOTIF. JRNL REF J.MOL.BIOL. V. 294 1327 1999 JRNL REFN ISSN 0022-2836 JRNL PMID 10600388 JRNL DOI 10.1006/JMBI.1999.3383 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 1.3, X-PLOR 3.1 REMARK 3 AUTHORS : BRUKER (XWINNMR), BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES WERE GENERATED USING 564 REMARK 3 INTER-PROTON DISTANCE RESTRAINTS DERIVED FROM 230 INTRA-RESIDUAL, REMARK 3 141 SEQUENTIAL, 108 MEDIUM RANGE AND 85 LONG RANGE NOE REMARK 3 INTENSITIES. THESE DISTANCE RESTRAINTS WERE SUPPLEMENTED WITH 17 REMARK 3 BACKBONE AND 7 SIDE-CHAIN DIHEDRAL ANGLE RESTRAINTS FROM SPIN- REMARK 3 SPIN COUPLING CONSTANTS. REMARK 4 REMARK 4 1DF6 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-NOV-99. REMARK 100 THE DEPOSITION ID IS D_1000010033. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 3.6 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.6MM CYCLOVIOLACIN O1 1H; 1.6MM REMARK 210 CYCLOVIOLACIN O1 1H REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; DQF-COSY; TOCSY; E REMARK 210 -COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : AMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 1.3, X-PLOR 3.1 REMARK 210 METHOD USED : DISTANCE GEOMETRY, SIMULATED REMARK 210 ANNEALING, MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 16 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE REMARK 210 COVALENT GEOMETRY,STRUCTURES REMARK 210 WITH THE LEAST RESTRAINT REMARK 210 VIOLATIONS,STRUCTURES WITH THE REMARK 210 LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 16 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D REMARK 210 HOMONUCLEAR TECHNIQUES. 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 ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 3 CYS A 22 CA - CB - SG ANGL. DEV. = 7.3 DEGREES REMARK 500 10 CYS A 2 CA - CB - SG ANGL. DEV. = 7.5 DEGREES REMARK 500 15 CYS A 22 CA - CB - SG ANGL. DEV. = 6.7 DEGREES 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 VAL A 3 -55.85 -24.77 REMARK 500 1 TYR A 4 -55.19 -126.54 REMARK 500 1 PRO A 6 -174.88 -55.19 REMARK 500 1 VAL A 9 -40.34 -141.29 REMARK 500 1 CYS A 17 85.73 -62.47 REMARK 500 1 CYS A 28 23.21 -141.68 REMARK 500 1 ALA A 29 -176.16 63.68 REMARK 500 2 VAL A 3 -54.97 -26.59 REMARK 500 2 TYR A 4 -58.05 -125.51 REMARK 500 2 PRO A 6 -177.09 -58.81 REMARK 500 2 THR A 8 42.15 39.13 REMARK 500 2 VAL A 9 -66.26 -149.41 REMARK 500 2 CYS A 17 85.21 -63.70 REMARK 500 2 ASN A 24 61.95 -150.21 REMARK 500 2 CYS A 28 25.53 -144.78 REMARK 500 2 ALA A 29 171.78 65.97 REMARK 500 3 VAL A 3 -61.00 -22.55 REMARK 500 3 CYS A 7 -49.59 179.34 REMARK 500 3 THR A 8 26.68 36.27 REMARK 500 3 VAL A 9 -55.15 -145.38 REMARK 500 3 ASN A 24 57.13 -145.12 REMARK 500 3 ALA A 29 -176.04 73.52 REMARK 500 4 VAL A 3 -57.62 -23.09 REMARK 500 4 TYR A 4 -56.97 -125.72 REMARK 500 4 PRO A 6 -176.80 -59.39 REMARK 500 4 THR A 8 37.29 39.05 REMARK 500 4 VAL A 9 -63.12 -141.57 REMARK 500 4 CYS A 17 82.77 -65.66 REMARK 500 4 CYS A 28 19.15 -142.19 REMARK 500 4 ALA A 29 172.94 69.06 REMARK 500 5 VAL A 3 -56.00 -25.48 REMARK 500 5 TYR A 4 -57.31 -125.07 REMARK 500 5 PRO A 6 -177.40 -59.74 REMARK 500 5 THR A 8 40.99 37.21 REMARK 500 5 VAL A 9 -67.87 -145.23 REMARK 500 5 CYS A 17 85.61 -63.04 REMARK 500 5 CYS A 28 23.21 -143.04 REMARK 500 5 ALA A 29 174.65 69.75 REMARK 500 6 CYS A 2 57.07 -104.61 REMARK 500 6 TYR A 4 -58.25 -122.14 REMARK 500 6 PRO A 6 -178.81 -58.92 REMARK 500 6 VAL A 9 -65.22 -142.92 REMARK 500 6 CYS A 17 92.48 -64.40 REMARK 500 6 CYS A 28 27.90 -146.28 REMARK 500 6 ALA A 29 175.86 67.08 REMARK 500 7 VAL A 3 -55.20 -26.21 REMARK 500 7 TYR A 4 -58.14 -125.31 REMARK 500 7 PRO A 6 -174.92 -57.88 REMARK 500 7 VAL A 9 -37.02 -145.58 REMARK 500 7 CYS A 17 85.10 -66.70 REMARK 500 REMARK 500 THIS ENTRY HAS 116 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1DF6 A 1 24 UNP P82230 CYO1_VIOOD 7 30 SEQRES 1 A 30 SER CYS VAL TYR ILE PRO CYS THR VAL THR ALA LEU LEU SEQRES 2 A 30 GLY CYS SER CYS SER ASN ARG VAL CYS TYR ASN GLY ILE SEQRES 3 A 30 PRO CYS ALA GLU HELIX 1 1 THR A 10 GLY A 14 5 5 SHEET 1 A 2 SER A 16 SER A 18 0 SHEET 2 A 2 VAL A 21 TYR A 23 -1 O VAL A 21 N SER A 18 SSBOND 1 CYS A 2 CYS A 17 1555 1555 2.02 SSBOND 2 CYS A 7 CYS A 22 1555 1555 2.02 SSBOND 3 CYS A 15 CYS A 28 1555 1555 2.02 LINK N SER A 1 C GLU A 30 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