HEADER ANTIFUNGAL PROTEIN 21-MAR-12 2LR3 TITLE SOLUTION STRUCTURE OF THE ANTI-FUNGAL DEFENSIN DEF4 (MTR_8G070770) TITLE 2 FROM MEDICAGO TRUNCATULA (BARREL CLOVER) COMPND MOL_ID: 1; COMPND 2 MOLECULE: DEFENSIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 30-76; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MEDICAGO TRUNCATULA; SOURCE 3 ORGANISM_COMMON: BARREL MEDIC; SOURCE 4 ORGANISM_TAXID: 3880; SOURCE 5 STRAIN: A17; SOURCE 6 GENE: MTR_049S0004, MTR_8G070770; SOURCE 7 EXPRESSION_SYSTEM: PICHIA PASTORIS; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 4922; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PPIC9 KEYWDS FUNGAL DISEASE, ANTIFUNGAL AGENT, ANTIFUNGAL PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR G.W.BUCHKO,T.J.SMITH,D.M.SHAH REVDAT 3 14-JUN-23 2LR3 1 REMARK REVDAT 2 18-DEC-13 2LR3 1 JRNL REVDAT 1 26-SEP-12 2LR3 0 JRNL AUTH U.S.SAGARAM,K.EL-MOUNADI,G.W.BUCHKO,H.R.BERG,J.KAUR, JRNL AUTH 2 R.S.PANDURANGI,T.J.SMITH,D.M.SHAH JRNL TITL STRUCTURAL AND FUNCTIONAL STUDIES OF A PHOSPHATIDIC JRNL TITL 2 ACID-BINDING ANTIFUNGAL PLANT DEFENSIN MTDEF4: JRNL TITL 3 IDENTIFICATION OF AN RGFRRR MOTIF GOVERNING FUNGAL CELL JRNL TITL 4 ENTRY. JRNL REF PLOS ONE V. 8 82485 2013 JRNL REFN ESSN 1932-6203 JRNL PMID 24324798 JRNL DOI 10.1371/JOURNAL.PONE.0082485 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SPARKY 3.115, CNS 1.1, CYANA 2.1 REMARK 3 AUTHORS : GODDARD (SPARKY), BRUNGER, ADAMS, CLORE, GROS, REMARK 3 NILGES AND READ (CNS), GUNTERT, MUMENTHALER AND REMARK 3 WUTHRICH (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURE DETERMINATION WAS PERFORMED REMARK 3 ITERATIVELY USING CYANA (AUTOMATED NOESY ASSIGNMENTS). A TOTAL REMARK 3 OF 20 STRUCTURES OUT OF 100 WITH LOWEST TARGET FUNCTION FROM THE REMARK 3 FINAL CYANA CALCULATION WERE TAKEN AND REFINED BY RESTRAINED REMARK 3 MOLECULAR DYNAMICS/ENERGY MINIMIZATION IN EXPLICIT WATER (CNS) REMARK 3 AFTER ADDING 0% TO THE UPPER BOUNDARY LIMIT OF THE DISTANCE REMARK 3 RESTRAINTS AND THE VDW LIMIT TO THE LOWER RESTRAINT. PARAM19 WAS REMARK 3 USED FOR THE WATER REFINEMENT CALCULATIONS. OXIDATION OF ALL THE REMARK 3 CYS RESIDUES WAS CONFIRMED BY THE C-BETA CHEMICAL SHIFTS FOR THE REMARK 3 CYS RESIDUES DETERMINED FROM A NATURAL ABUNDANCE 1H-13C-HSQC REMARK 3 SPECTRUM. RESTRAINTS FOR THE DISFULFIDE BONDS WERE INTRODUCED ON REMARK 3 THE BASIS OF POSITION IN SIMILAR SEQUENCES. REMARK 4 REMARK 4 2LR3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-APR-12. REMARK 100 THE DEPOSITION ID IS D_1000102727. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 4.4 REMARK 210 IONIC STRENGTH : 0.01 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM [U-99% 15N] PROTEIN, 0.01 REMARK 210 MM TRIS, 93% H2O/7% D2O; 1 MM REMARK 210 PROTEIN, 0.01 MM TRIS, 93% H2O/7% REMARK 210 D2O; 1 MM [U-99% 15N] PROTEIN, REMARK 210 0.01 MM TRIS, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 2D 1H-1H TOCSY; 2D 1H-1H NOESY; REMARK 210 3D 1H-15N NOESY; 3D 1H-15N TOCSY; REMARK 210 DEUTERIUM EXCHANGE REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 750 MHZ REMARK 210 SPECTROMETER MODEL : INOVA; VNMRS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY 3.115, FELIX 2007, CYANA REMARK 210 2.1, PSVS 1.3 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION 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 SER A 30 114.78 -165.64 REMARK 500 1 PHE A 37 137.02 176.91 REMARK 500 1 ARG A 38 -27.40 72.96 REMARK 500 2 SER A 5 -169.89 -117.24 REMARK 500 2 PHE A 29 92.17 -63.79 REMARK 500 2 SER A 30 117.04 -167.89 REMARK 500 3 CYS A 14 88.76 -65.28 REMARK 500 3 ARG A 28 122.27 -172.71 REMARK 500 3 PHE A 29 101.80 -44.08 REMARK 500 3 ARG A 39 78.10 56.78 REMARK 500 4 CYS A 14 85.62 -62.50 REMARK 500 4 GLU A 27 -78.13 -64.49 REMARK 500 4 ARG A 28 -41.12 -153.86 REMARK 500 5 PRO A 13 43.00 -77.71 REMARK 500 5 CYS A 14 108.34 64.00 REMARK 500 5 SER A 30 112.94 -162.92 REMARK 500 6 SER A 30 116.68 -165.30 REMARK 500 6 PHE A 37 -87.43 -92.60 REMARK 500 6 ARG A 39 110.83 -177.59 REMARK 500 7 SER A 5 -169.47 -101.30 REMARK 500 7 SER A 16 136.53 -173.09 REMARK 500 7 ARG A 28 -91.00 -168.59 REMARK 500 7 PHE A 37 93.90 -63.68 REMARK 500 7 ARG A 40 93.76 58.02 REMARK 500 8 ALA A 15 -40.51 -151.97 REMARK 500 8 SER A 16 145.15 -177.07 REMARK 500 8 PHE A 29 84.02 -65.96 REMARK 500 8 SER A 30 117.37 -163.44 REMARK 500 9 ARG A 28 143.16 -171.81 REMARK 500 9 PHE A 29 98.91 -60.43 REMARK 500 9 ARG A 39 77.62 56.22 REMARK 500 10 GLU A 27 -73.00 -71.21 REMARK 500 10 PHE A 29 101.95 -56.42 REMARK 500 11 LYS A 11 98.64 -59.68 REMARK 500 11 SER A 30 114.79 -177.03 REMARK 500 11 PHE A 37 -68.12 -132.63 REMARK 500 11 ARG A 39 -45.15 -149.95 REMARK 500 12 SER A 30 113.18 -162.98 REMARK 500 12 PHE A 37 -35.71 176.93 REMARK 500 12 ARG A 39 84.26 178.61 REMARK 500 13 SER A 16 119.46 -164.26 REMARK 500 13 SER A 30 115.10 -163.60 REMARK 500 14 SER A 30 119.38 -161.92 REMARK 500 15 CYS A 14 93.84 -60.69 REMARK 500 15 ARG A 39 70.07 56.42 REMARK 500 16 PHE A 10 -178.98 -69.67 REMARK 500 16 LYS A 11 36.36 -79.28 REMARK 500 16 PRO A 13 100.80 -54.63 REMARK 500 16 CYS A 14 108.38 -48.12 REMARK 500 16 SER A 30 115.25 -172.85 REMARK 500 REMARK 500 THIS ENTRY HAS 67 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 18345 RELATED DB: BMRB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE AUTHORS STATE THAT THE GENOMIC SEQUENCE IS CORRECT, HIS62. REMARK 999 DURING PCR GENERATION OF THE EXPRESSION CLONE, AN ARG WAS OBTAINED REMARK 999 IN THIS POSITION INSTEAD. DBREF 2LR3 A 1 47 UNP G7L736 G7L736_MEDTR 30 76 SEQADV 2LR3 ARG A 33 UNP G7L736 HIS 62 SEE REMARK 999 SEQRES 1 A 47 ARG THR CYS GLU SER GLN SER HIS LYS PHE LYS GLY PRO SEQRES 2 A 47 CYS ALA SER ASP HIS ASN CYS ALA SER VAL CYS GLN THR SEQRES 3 A 47 GLU ARG PHE SER GLY GLY ARG CYS ARG GLY PHE ARG ARG SEQRES 4 A 47 ARG CYS PHE CYS THR THR HIS CYS HELIX 1 1 SER A 16 ARG A 28 1 13 SHEET 1 A 3 THR A 2 GLN A 6 0 SHEET 2 A 3 CYS A 41 HIS A 46 -1 O THR A 45 N CYS A 3 SHEET 3 A 3 GLY A 31 CYS A 34 -1 N ARG A 33 O PHE A 42 SSBOND 1 CYS A 3 CYS A 47 1555 1555 2.03 SSBOND 2 CYS A 14 CYS A 34 1555 1555 2.03 SSBOND 3 CYS A 20 CYS A 41 1555 1555 2.03 SSBOND 4 CYS A 24 CYS A 43 1555 1555 2.04 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