HEADER ANTIMICROBIAL PROTEIN 23-JUN-22 8DFZ TITLE NMR SHOWS WHY A SMALL CHEMICAL CHANGE ALMOST ABOLISHES THE TITLE 2 ANTIMICROBIAL ACTIVITY OF GCCF COMPND MOL_ID: 1; COMPND 2 MOLECULE: BACTERIOCIN GLYCOCIN F; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: GCCF; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LACTIPLANTIBACILLUS PLANTARUM; SOURCE 3 ORGANISM_TAXID: 1590; SOURCE 4 GENE: GCCF; SOURCE 5 EXPRESSION_SYSTEM: LACTIPLANTIBACILLUS PLANTARUM; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 1590 KEYWDS GCCF, ANTIMICROBIAL, BACTERIOSTATIC, ANTIMICROBIAL PROTEIN EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR E.HARJES,P.J.B.EDWARDS,G.NORRIS REVDAT 3 13-SEP-23 8DFZ 1 JRNL REVDAT 2 16-AUG-23 8DFZ 1 JRNL REVDAT 1 05-JUL-23 8DFZ 0 JRNL AUTH E.HARJES,P.J.B.EDWARDS,S.W.BISSET,M.L.PATCHETT,G.B.JAMESON, JRNL AUTH 2 S.H.YANG,C.D.NAVO,P.W.R.HARRIS,M.A.BRIMBLE,G.E.NORRIS JRNL TITL NMR SHOWS WHY A SMALL CHEMICAL CHANGE ALMOST ABOLISHES THE JRNL TITL 2 ANTIMICROBIAL ACTIVITY OF GLYCOCIN F. JRNL REF BIOCHEMISTRY V. 62 2669 2023 JRNL REFN ISSN 0006-2960 JRNL PMID 37531216 JRNL DOI 10.1021/ACS.BIOCHEM.3C00197 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : YASARA REMARK 3 AUTHORS : ELMER KRIEGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8DFZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-JUN-22. REMARK 100 THE DEPOSITION ID IS D_1000266548. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 307 REMARK 210 PH : 0 REMARK 210 IONIC STRENGTH : 0 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1 MM NATURAL ABUNDABNCE GCCF REMARK 210 MODIFIED, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : TOCSY; 2D 1H-1H NOESY; 2D DQF REMARK 210 -COSY; 2D 1H-13C HSQC; HMBC; 3D REMARK 210 1H-13C TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ REMARK 210 SPECTROMETER MODEL : BRUKER AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : YASARA, CARA, ATNOS REMARK 210 METHOD USED : SIMULATED ANNEALING 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: 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: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 1 MET A 24 N - CA - CB ANGL. DEV. = -11.5 DEGREES REMARK 500 3 MET A 24 N - CA - CB ANGL. DEV. = -10.9 DEGREES REMARK 500 6 MET A 24 N - CA - CB ANGL. DEV. = -10.9 DEGREES REMARK 500 7 MET A 24 N - CA - CB ANGL. DEV. = -11.2 DEGREES REMARK 500 10 MET A 24 N - CA - CB ANGL. DEV. = -11.0 DEGREES 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 ASP A 17 -95.87 24.82 REMARK 500 1 THR A 20 -62.01 -105.48 REMARK 500 1 HIS A 33 70.34 -118.19 REMARK 500 1 SER A 40 51.67 -117.17 REMARK 500 1 HIS A 42 32.27 -151.67 REMARK 500 2 ASP A 17 -89.98 22.23 REMARK 500 2 THR A 20 -61.87 -101.49 REMARK 500 2 HIS A 34 22.18 -151.07 REMARK 500 2 SER A 39 29.47 -151.85 REMARK 500 2 TYR A 41 -69.54 61.17 REMARK 500 2 HIS A 42 24.09 -141.11 REMARK 500 3 ASP A 17 -86.67 31.34 REMARK 500 3 THR A 20 -62.30 -103.25 REMARK 500 3 HIS A 34 17.79 -153.94 REMARK 500 3 TYR A 41 -33.06 65.04 REMARK 500 4 ASP A 17 -88.99 23.78 REMARK 500 4 THR A 20 -62.06 -101.50 REMARK 500 4 TYR A 41 -51.66 65.79 REMARK 500 4 HIS A 42 19.01 -142.48 REMARK 500 5 ASP A 17 -87.85 36.46 REMARK 500 5 THR A 20 -62.30 -102.75 REMARK 500 5 HIS A 34 42.96 -149.40 REMARK 500 5 SER A 40 48.80 -73.96 REMARK 500 6 ASP A 17 -88.43 33.32 REMARK 500 6 THR A 20 -61.99 -102.84 REMARK 500 6 SER A 36 -161.72 58.27 REMARK 500 6 SER A 39 18.20 55.34 REMARK 500 6 TYR A 41 21.21 -73.01 REMARK 500 6 HIS A 42 25.14 -141.82 REMARK 500 7 ASP A 17 -93.59 36.68 REMARK 500 7 THR A 20 -62.29 -102.91 REMARK 500 7 HIS A 34 40.40 -150.34 REMARK 500 7 SER A 38 156.01 70.88 REMARK 500 7 SER A 39 6.95 59.09 REMARK 500 7 HIS A 42 22.53 -144.56 REMARK 500 8 ASP A 17 -88.81 23.85 REMARK 500 8 THR A 20 -62.24 -101.21 REMARK 500 8 HIS A 33 52.54 -109.96 REMARK 500 8 HIS A 42 19.44 -151.93 REMARK 500 9 ASP A 17 -89.69 21.86 REMARK 500 9 THR A 20 -62.31 -100.98 REMARK 500 9 HIS A 33 77.39 -119.24 REMARK 500 9 HIS A 34 40.13 -151.74 REMARK 500 9 HIS A 42 20.74 -146.85 REMARK 500 10 ASP A 17 -89.25 23.22 REMARK 500 10 THR A 20 -62.45 -102.15 REMARK 500 10 HIS A 34 39.24 -153.35 REMARK 500 10 HIS A 42 31.15 -160.52 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2KUY RELATED DB: PDB REMARK 900 SAME PEPTIDE WITHOUT SER 18 MODIFICATION REMARK 900 RELATED ID: 31028 RELATED DB: BMRB REMARK 900 NMR SHOWS WHY A SMALL CHEMICAL CHANGE ALMOST ABOLISHES THE REMARK 900 ANTIMICROBIAL ACTIVITY OF GCCF DBREF 8DFZ A 1 43 UNP E9K9Z1 GCCF_LACPN 22 64 SEQRES 1 A 43 LYS PRO ALA TRP CYS TRP TYR THR LEU ALA MET CYS GLY SEQRES 2 A 43 ALA GLY TYR ASP EW6 GLY THR CYS ASP TYR MET TYR SER SEQRES 3 A 43 HIS CYS PHE GLY ILE LYS HIS HIS SER SER GLY SER SER SEQRES 4 A 43 SER TYR HIS CYS MODRES 8DFZ EW6 A 18 SER MODIFIED RESIDUE HET EW6 A 18 13 HET NAG A 101 28 HET NAG A 102 28 HETNAM EW6 ALPHA-METHYL-L-SERINE HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETSYN EW6 (2S)-2-AZANYL-2-METHYL-3-OXIDANYL-PROPANOIC ACID HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 1 EW6 C4 H9 N O3 FORMUL 2 NAG 2(C8 H15 N O6) HELIX 1 AA1 PRO A 2 CYS A 12 1 11 HELIX 2 AA2 GLY A 13 GLY A 15 5 3 HELIX 3 AA3 THR A 20 PHE A 29 1 10 SSBOND 1 CYS A 5 CYS A 28 1555 1555 2.02 SSBOND 2 CYS A 12 CYS A 21 1555 1555 2.02 LINK C ASP A 17 N EW6 A 18 1555 1555 1.38 LINK C EW6 A 18 N GLY A 19 1555 1555 1.34 LINK OG EW6 A 18 C1 NAG A 101 1555 1555 1.46 LINK SG CYS A 43 C1 NAG A 102 1555 1555 1.87 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 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