10 20 30 40 50 60 70 80 2GL1 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER 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 KEYWDS 2 ALFA/BETA MOTIF, 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 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 JRNL TITL 2 ALPHA-AMYLASE INHIBITORY ACTIVITY OF PLANT JRNL TITL 3 DEFENSIN. JRNL REF PROTEINS V. 68 530 2007 JRNL REFN ISSN 0887-3585 JRNL PMID 17444520 JRNL DOI 10.1002/PROT.21378
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : 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. REMARK 3 ULRICH,ROBERT KAPTEIN, AND ALEXANDRE M.J.J. REMARK 3 BONVIN 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 RCSB ID CODE IS RCSB037250.
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 REMARK 210 PHOSPHATE 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 : XWINNMR 3.5, SPARKY 3.111, REMARK 210 CNS 1.1 REMARK 210 METHOD USED : SIMULATED ANNEALING WITH REMARK 210 TORSION ANGLE DYNAMICS AND REMARK 210 SUBSEQUENT REFINEMENT WITH REMARK 210 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, REMARK 210 STRUCTURES WITH THE LOWEST REMARK 210 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 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