HEADER PLANT PROTEIN 04-APR-06 2GL1 TITLE NMR SOLUTION STRUCTURE OF VIGNA RADIATA DEFENSIN 2 (VRD2) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PDF1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 1-47; COMPND 5 SYNONYM: DEFENSIN 2 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIGNA RADIATA; SOURCE 3 ORGANISM_TAXID: 157791 KEYWDS ANTIMICROBIAL, PLANT DEFENSIN, CYSTEINE-STABILIZED ALFA/BETA MOTIF, KEYWDS 2 PLANT PROTEIN EXPDTA SOLUTION NMR NUMMDL 18 AUTHOR K.F.LIN,T.R.LEE,P.H.TSAI,M.P.HSU,C.S.CHEN,P.C.LYU REVDAT 4 09-MAR-22 2GL1 1 REMARK REVDAT 3 24-FEB-09 2GL1 1 VERSN REVDAT 2 27-NOV-07 2GL1 1 JRNL AUTHOR REVDAT 1 03-APR-07 2GL1 0 JRNL AUTH K.F.LIN,T.R.LEE,P.H.TSAI,M.P.HSU,C.S.CHEN,P.C.LYU JRNL TITL STRUCTURE-BASED PROTEIN ENGINEERING FOR ALPHA-AMYLASE JRNL TITL 2 INHIBITORY ACTIVITY OF PLANT DEFENSIN. JRNL REF PROTEINS V. 68 530 2007 JRNL REFN ISSN 0887-3585 JRNL PMID 17444520 JRNL DOI 10.1002/PROT.21378 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 3.5, RECOORD REMARK 3 AUTHORS : AART J. NEDERVEEN, JURGEN F. DORELEIJERS, WIM REMARK 3 VRANKEN, ZACHARY MILLER, CHRIS A.E.M. SPRONK REMARK 3 SANDER B. NABUURS, PETER GU NTERT, MIRON LIVNY, REMARK 3 JOHN L. MARKLEY, MICHAEL NILGES, ELDON L. ULRICH, REMARK 3 ROBERT KAPTEIN, AND ALEXANDRE M.J.J. BONVIN REMARK 3 (RECOORD) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2GL1 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-APR-06. REMARK 100 THE DEPOSITION ID IS D_1000037250. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 288 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 50MM SODIUM PHOSPHATE REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 2MM VRD2, 50MM SODIUM PHOSPHATE REMARK 210 NA; 90% H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY; DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY 3.111, CNS 1.1 REMARK 210 METHOD USED : SIMULATED ANNEALING WITH TORSION REMARK 210 ANGLE DYNAMICS AND SUBSEQUENT REMARK 210 REFINEMENT WITH RECOORD REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 18 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS,STRUCTURES REMARK 210 WITH THE LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 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: 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 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 4 THR A 2 117.51 61.73 REMARK 500 4 PHE A 15 -70.17 -92.17 REMARK 500 4 LEU A 30 -165.46 -102.81 REMARK 500 6 THR A 2 117.03 62.11 REMARK 500 7 THR A 2 116.49 63.34 REMARK 500 7 ASP A 38 9.17 -163.14 REMARK 500 7 PHE A 39 19.01 56.21 REMARK 500 8 PHE A 15 -61.00 -136.88 REMARK 500 8 ASP A 38 -3.83 77.27 REMARK 500 8 PHE A 39 15.08 -171.76 REMARK 500 9 THR A 2 112.36 47.70 REMARK 500 12 THR A 2 121.92 63.52 REMARK 500 12 LEU A 30 -169.08 -105.78 REMARK 500 13 THR A 2 130.85 69.17 REMARK 500 13 PHE A 15 -50.15 -127.12 REMARK 500 15 THR A 2 113.62 60.40 REMARK 500 15 PHE A 15 -38.22 -132.50 REMARK 500 16 ASP A 37 1.23 -66.79 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 6 ARG A 31 0.10 SIDE CHAIN REMARK 500 8 ARG A 31 0.07 SIDE CHAIN REMARK 500 9 ARG A 36 0.08 SIDE CHAIN REMARK 500 12 ARG A 36 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 2GL1 A 1 47 GB 18146788 BAB82453 29 75 SEQRES 1 A 47 LYS THR CYS GLU ASN LEU ALA ASN THR TYR ARG GLY PRO SEQRES 2 A 47 CYS PHE THR THR GLY SER CYS ASP ASP HIS CYS LYS ASN SEQRES 3 A 47 LYS GLU HIS LEU ARG SER GLY ARG CYS ARG ASP ASP PHE SEQRES 4 A 47 ARG CYS TRP CYS THR ARG ASN CYS HELIX 1 1 THR A 16 LYS A 27 1 12 SHEET 1 A 3 THR A 2 LEU A 6 0 SHEET 2 A 3 CYS A 41 ASN A 46 -1 O ARG A 45 N CYS A 3 SHEET 3 A 3 SER A 32 CYS A 35 -1 N ARG A 34 O TRP A 42 SSBOND 1 CYS A 3 CYS A 47 1555 1555 2.04 SSBOND 2 CYS A 14 CYS A 35 1555 1555 2.03 SSBOND 3 CYS A 20 CYS A 41 1555 1555 2.01 SSBOND 4 CYS A 24 CYS A 43 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