PDB Short entry for 1DKC HEADER ANTIFUNGAL PROTEIN 07-DEC-99 1DKC TITLE SOLUTION STRUCTURE OF PAFP-S, AN ANTIFUNGAL PEPTIDE FROM THE SEEDS OF TITLE 2 PHYTOLACCA AMERICANA COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANTIFUNGAL PEPTIDE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PAFP-S SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PHYTOLACCA AMERICANA; SOURCE 3 ORGANISM_COMMON: AMERICAN POKEWEED; SOURCE 4 ORGANISM_TAXID: 3527; SOURCE 5 OTHER_DETAILS: SEED KEYWDS THREE-STRANDS BETA SHEET, ANTIFUNGAL PROTEIN EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR D.C.WANG,G.H.GAO,F.SHAO,J.X.DAI,J.F.WANG REVDAT 4 16-FEB-22 1DKC 1 REMARK REVDAT 3 24-FEB-09 1DKC 1 VERSN REVDAT 2 15-MAR-05 1DKC 1 JRNL REVDAT 1 13-DEC-00 1DKC 0 JRNL AUTH G.H.GAO,W.LIU,J.X.DAI,J.F.WANG,Z.HU,Y.ZHANG,D.C.WANG JRNL TITL SOLUTION STRUCTURE OF PAFP-S: A NEW KNOTTIN-TYPE ANTIFUNGAL JRNL TITL 2 PEPTIDE FROM THE SEEDS OF PHYTOLACCA AMERICANA JRNL REF BIOCHEMISTRY V. 40 10973 2001 JRNL REFN ISSN 0006-2960 JRNL PMID 11551192 JRNL DOI 10.1021/BI010167K REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : UXNMR 1.0, X-PLOR 3.851 REMARK 3 AUTHORS : BRUKER (UXNMR), BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1DKC COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-DEC-99. REMARK 100 THE DEPOSITION ID IS D_1000010155. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300 REMARK 210 PH : 3.5 REMARK 210 IONIC STRENGTH : NA REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 4MM PROTEIN, 0.2 MM DSS; 4MM REMARK 210 PROTEIN, 0.2 MM DSS REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; DQF-COSY; 2D COSY; 2D REMARK 210 TOCSY; E-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 97 REMARK 210 METHOD USED : SIMULATED ANNEALING MOLECULAR REMARK 210 DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 30 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : 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 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (RES=RESIDUE NAME; REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 470 MODELS 1-10 REMARK 470 RES CSSEQI ATOMS REMARK 470 ARG A 38 O 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 HZ3 LYS A 5 OG SER A 21 1.31 REMARK 500 HZ2 LYS A 36 OD1 ASN A 37 1.33 REMARK 500 OD1 ASN A 6 HZ1 LYS A 36 1.34 REMARK 500 OG SER A 22 HH22 ARG A 38 1.38 REMARK 500 HG SER A 13 OG SER A 31 1.39 REMARK 500 H PHE A 25 O VAL A 34 1.47 REMARK 500 HZ2 LYS A 5 O CYS A 20 1.53 REMARK 500 O GLY A 8 H CYS A 35 1.54 REMARK 500 HH12 ARG A 9 OD1 ASN A 11 1.55 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 PRO A 17 -78.51 -75.91 REMARK 500 1 SER A 22 -4.14 71.13 REMARK 500 1 ASN A 37 -167.30 -76.66 REMARK 500 2 LYS A 5 -72.94 -76.71 REMARK 500 2 SER A 21 -73.49 -98.93 REMARK 500 2 SER A 22 23.74 -174.33 REMARK 500 3 SER A 21 -75.46 -112.90 REMARK 500 3 SER A 22 14.12 -172.38 REMARK 500 3 GLN A 30 -80.26 -151.79 REMARK 500 3 SER A 31 71.66 174.33 REMARK 500 3 ASN A 37 -76.81 -60.60 REMARK 500 4 ASN A 6 51.37 -97.42 REMARK 500 4 ALA A 14 -71.38 -121.16 REMARK 500 4 SER A 21 -73.36 -101.10 REMARK 500 4 SER A 22 18.65 -168.90 REMARK 500 4 ASN A 37 -83.57 -69.34 REMARK 500 5 PRO A 17 -164.52 -74.16 REMARK 500 5 SER A 21 -75.00 -101.11 REMARK 500 5 SER A 22 18.48 -175.64 REMARK 500 6 SER A 13 44.57 -101.78 REMARK 500 6 SER A 22 -3.17 83.68 REMARK 500 6 ASN A 37 -80.79 -55.23 REMARK 500 7 ASN A 11 -169.91 -166.41 REMARK 500 7 SER A 22 -5.04 84.27 REMARK 500 7 ASN A 37 -89.57 -68.40 REMARK 500 8 ALA A 14 -70.92 -129.79 REMARK 500 8 SER A 21 -75.39 -109.90 REMARK 500 8 SER A 22 25.34 -170.46 REMARK 500 8 SER A 31 60.46 70.61 REMARK 500 9 ASN A 11 -169.91 -160.21 REMARK 500 9 SER A 21 -73.23 -107.46 REMARK 500 9 SER A 22 15.84 -171.17 REMARK 500 9 ASN A 37 -76.01 -75.51 REMARK 500 10 ASN A 11 -141.88 -161.19 REMARK 500 10 SER A 13 -166.52 -126.83 REMARK 500 10 PRO A 17 40.62 -96.49 REMARK 500 10 SER A 21 -72.27 -99.28 REMARK 500 10 SER A 22 13.17 -173.37 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 1 ARG A 9 0.31 SIDE CHAIN REMARK 500 1 ARG A 38 0.31 SIDE CHAIN REMARK 500 2 ARG A 9 0.32 SIDE CHAIN REMARK 500 2 ARG A 38 0.29 SIDE CHAIN REMARK 500 3 ARG A 9 0.32 SIDE CHAIN REMARK 500 3 ARG A 38 0.28 SIDE CHAIN REMARK 500 4 ARG A 9 0.31 SIDE CHAIN REMARK 500 4 ARG A 38 0.29 SIDE CHAIN REMARK 500 5 ARG A 9 0.31 SIDE CHAIN REMARK 500 5 ARG A 38 0.29 SIDE CHAIN REMARK 500 6 ARG A 9 0.29 SIDE CHAIN REMARK 500 6 ARG A 38 0.29 SIDE CHAIN REMARK 500 7 ARG A 9 0.31 SIDE CHAIN REMARK 500 7 ARG A 38 0.31 SIDE CHAIN REMARK 500 8 ARG A 9 0.29 SIDE CHAIN REMARK 500 8 ARG A 38 0.26 SIDE CHAIN REMARK 500 9 ARG A 9 0.30 SIDE CHAIN REMARK 500 9 ARG A 38 0.27 SIDE CHAIN REMARK 500 10 ARG A 9 0.26 SIDE CHAIN REMARK 500 10 ARG A 38 0.26 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1DKC A 1 38 UNP P81418 PAFP_PHYAM 28 65 SEQRES 1 A 38 ALA GLY CYS ILE LYS ASN GLY GLY ARG CYS ASN ALA SER SEQRES 2 A 38 ALA GLY PRO PRO TYR CYS CYS SER SER TYR CYS PHE GLN SEQRES 3 A 38 ILE ALA GLY GLN SER TYR GLY VAL CYS LYS ASN ARG SHEET 1 A 3 GLY A 8 CYS A 10 0 SHEET 2 A 3 TYR A 32 LYS A 36 -1 O GLY A 33 N CYS A 10 SHEET 3 A 3 TYR A 23 ILE A 27 -1 N TYR A 23 O LYS A 36 SSBOND 1 CYS A 3 CYS A 20 1555 1555 2.03 SSBOND 2 CYS A 10 CYS A 24 1555 1555 2.02 SSBOND 3 CYS A 19 CYS A 35 1555 1555 2.02 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