HEADER TOXIN 26-JAN-00 1ED0 TITLE NMR STRUCTURAL DETERMINATION OF VISCOTOXIN A3 FROM VISCUM ALBUM L. COMPND MOL_ID: 1; COMPND 2 MOLECULE: VISCOTOXIN A3; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VISCUM ALBUM; SOURCE 3 ORGANISM_COMMON: EUROPEAN MISTLETOE; SOURCE 4 ORGANISM_TAXID: 3972 KEYWDS THIONIN, CONCENTRIC MOTIF, HELIX-TURN-HELIX, ALPHA-BETA PROTEIN, KEYWDS 2 AMPHIPATHIC HELIX, TOXIN EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR S.ROMAGNOLI,R.UGOLINI,F.FOGOLARI,G.SCHALLER,K.URECH,M.GIANNATTASIO, AUTHOR 2 L.RAGONA,H.MOLINARI REVDAT 4 16-FEB-22 1ED0 1 REMARK REVDAT 3 24-FEB-09 1ED0 1 VERSN REVDAT 2 05-APR-05 1ED0 3 ATOM JRNL REVDAT 1 04-FEB-00 1ED0 0 JRNL AUTH S.ROMAGNOLI,R.UGOLINI,F.FOGOLARI,G.SCHALLER,K.URECH, JRNL AUTH 2 M.GIANNATTASIO,L.RAGONA,H.MOLINARI JRNL TITL NMR STRUCTURAL DETERMINATION OF VISCOTOXIN A3 FROM VISCUM JRNL TITL 2 ALBUM L. JRNL REF BIOCHEM.J. V. 350 569 2000 JRNL REFN ISSN 0264-6021 JRNL PMID 10947973 JRNL DOI 10.1042/0264-6021:3500569 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DYANA 1.4, DISCOVER 98 REMARK 3 AUTHORS : GUENTERT, WUETHRICH (DYANA), MSI (DISCOVER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 1010 DISTANCE RESTRAINTS WERE REMARK 3 CALCULATED REDUCED TO 734 (230 INTRARESIDUE, 172 SEQUENTIAL, 191 REMARK 3 MEDIUM RANGE, 141 LONG RANGE) AFTER REMOVAL OF IRRELEVANT REMARK 3 RESTRAINTS. CALCULATION STARTED WITH 200 RANDOMIZED CONFORMERS REMARK 3 AND CONSISTENTLY VIOLATED RESTRAINTS WERE CHECKED AND RELAXED REMARK 3 WHERE NECESSARY. THIS PROCEDURE WAS REPEATED UNTIL NO CONSISTENT REMARK 3 VIOLATIONS WERE FOUND IN HALF OR MORE OF THE STRUCTURES. 600 NEW REMARK 3 CALCULATIONS WERE STARTED AND THE 20 STRUCTURES WITH LOWEST REMARK 3 TARGET FUNCTION WERE ANALYZED. THE STRUCTURE WITH LOWEST TARGET REMARK 3 FUNCTION AND THE STRUCTURE EXHIBITING THE LARGEST RMSD WITH IT REMARK 3 WERE SUBJECTED TO RESTRAINED MOLECULAR DYNAMICS (20 CYCLES OF 15 REMARK 3 PS RESTRAINED MOLECULAR DYNAMICS FOLLOWED BY MINIMIZATION). ALL REMARK 3 EVEN STRUCTURES FROM THE LAST 10 MINIMIZED STRUCTURES WERE REMARK 3 RETAINED FROM BOTH SETS AND DEPOSITED. REMARK 4 REMARK 4 1ED0 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-FEB-00. REMARK 100 THE DEPOSITION ID IS D_1000010459. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 285 REMARK 210 PH : 3.6 REMARK 210 IONIC STRENGTH : 50MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 2MM VISCOTOXIN A3 1H; 50MM REMARK 210 H3PO4/NAOH AQUEOUS BUFFER; 90% REMARK 210 H2O, 10% D2O; 2MM VISCOTOXIN A3 REMARK 210 1H; 50MM H3PO4/NAOH AQUEOUS REMARK 210 BUFFER; 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; DQF-COSY; TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 1.2, XEASY 1.2 REMARK 210 METHOD USED : RESTRAINED SIMULATED ANNEALING REMARK 210 IN TORSION ANGLE SPACE, REMARK 210 ITERATIVE RESTRAINTS REFINEMENT, REMARK 210 RESTRAINED MOLECULAR DYNAMICS IN REMARK 210 CARTESIAN COORDINATE SPACE REMARK 210 MINIMIZATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 600 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 8 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: 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 19 27.41 -79.71 REMARK 500 2 THR A 19 30.29 -80.81 REMARK 500 3 THR A 19 30.16 -80.61 REMARK 500 5 THR A 19 30.64 -80.13 REMARK 500 6 THR A 19 30.11 -80.69 REMARK 500 8 THR A 19 29.17 -79.87 REMARK 500 10 THR A 19 29.43 -79.97 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 2 TYR A 13 0.09 SIDE CHAIN REMARK 500 2 TYR A 44 0.12 SIDE CHAIN REMARK 500 4 TYR A 44 0.07 SIDE CHAIN REMARK 500 6 TYR A 44 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1CBN RELATED DB: PDB REMARK 900 CRAMBIN REMARK 900 RELATED ID: 1CNR RELATED DB: PDB REMARK 900 CRAMBIN REMARK 900 RELATED ID: 1CCM RELATED DB: PDB REMARK 900 CRAMBIN REMARK 900 RELATED ID: 1AB1 RELATED DB: PDB REMARK 900 CRAMBIN REMARK 900 RELATED ID: 2PLH RELATED DB: PDB REMARK 900 ALPHA-1-PUROTHIONIN REMARK 900 RELATED ID: 1BHP RELATED DB: PDB REMARK 900 BETA-PUROTHIONIN DBREF 1ED0 A 1 46 UNP P01538 THN3_VISAL 27 72 SEQRES 1 A 46 LYS SER CYS CYS PRO ASN THR THR GLY ARG ASN ILE TYR SEQRES 2 A 46 ASN ALA CYS ARG LEU THR GLY ALA PRO ARG PRO THR CYS SEQRES 3 A 46 ALA LYS LEU SER GLY CYS LYS ILE ILE SER GLY SER THR SEQRES 4 A 46 CYS PRO SER ASP TYR PRO LYS HELIX 1 1 THR A 7 LEU A 18 1 12 HELIX 2 2 ARG A 23 SER A 30 1 8 SHEET 1 A 2 SER A 2 CYS A 3 0 SHEET 2 A 2 LYS A 33 ILE A 34 -1 O LYS A 33 N CYS A 3 SSBOND 1 CYS A 3 CYS A 40 1555 1555 2.04 SSBOND 2 CYS A 4 CYS A 32 1555 1555 2.03 SSBOND 3 CYS A 16 CYS A 26 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