HEADER ANTIBIOTIC 09-JAN-23 8C5J TITLE SPATIAL STRUCTURE OF LCH-ALPHA PEPTIDE FROM TWO-COMPONENT LANTIBIOTIC TITLE 2 SYSTEM LICHENICIDIN VK21 CAVEAT 8C5J ABA A 12 HAS WRONG CHIRALITY AT ATOM CA ABA A 31 HAS WRONG CAVEAT 2 8C5J CHIRALITY AT ATOM CA ABA A 33 HAS WRONG CHIRALITY AT ATOM CAVEAT 3 8C5J CA COMPND MOL_ID: 1; COMPND 2 MOLECULE: LANTIBIOTIC LICHENICIDIN VK21 A1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: LCHA1; COMPND 5 OTHER_DETAILS: LICHENICIDIN VK21 IS A TETRACYCLIC PEPTIDE. THIOETHER COMPND 6 BONDS WITH CYSTEINE RESULT IN FOUR RINGS CROSSLINK 3-7 BETA- COMPND 7 METHYLLANTHIONINE (DBB-CYS) CROSSLINK 11-21 LANTHIONINE (DAL-CYS) COMPND 8 CROSSLINK 22-27 BETA-METHYLLANTHIONINE (DBB-CYS) CROSSLINK 24-31 COMPND 9 BETA-METHYLLANTHIONINE (DBB-CYS SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS LICHENIFORMIS; SOURCE 3 ORGANISM_TAXID: 1402; SOURCE 4 STRAIN: VK21 KEYWDS LICHENICIDIN VK21, LANTIBIOTICS, LCHA, ANTIBIOTIC, LANTHIONINE, KEYWDS 2 THIOESTER, TWO-COMPONENT LANTIBIOTIC SYSTEM EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR K.S.MINEEV,A.S.PARAMONOV,A.S.ARSENIEV,T.V.OVCHINNIKOVA,Z.O.SHENKAREV REVDAT 2 15-NOV-23 8C5J 1 LINK ATOM REVDAT 1 22-MAR-23 8C5J 0 SPRSDE 22-MAR-23 8C5J 2KTN JRNL AUTH I.S.PANINA,S.V.BALANDIN,A.V.TSAREV,A.O.CHUGUNOV,A.A.TAGAEV, JRNL AUTH 2 E.I.FINKINA,D.V.ANTOSHINA,E.V.SHEREMETEVA,A.S.PARAMONOV, JRNL AUTH 3 J.RICKMEYER,G.BIERBAUM,R.G.EFREMOV,Z.O.SHENKAREV, JRNL AUTH 4 T.V.OVCHINNIKOVA JRNL TITL SPECIFIC BINDING OF THE ALPHA-COMPONENT OF THE LANTIBIOTIC JRNL TITL 2 LICHENICIDIN TO THE PEPTIDOGLYCAN PRECURSOR LIPID II JRNL TITL 3 PREDETERMINES ITS ANTIMICROBIAL ACTIVITY. JRNL REF INT J MOL SCI V. 24 2023 JRNL REFN ESSN 1422-0067 JRNL PMID 36674846 JRNL DOI 10.3390/IJMS24021332 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH Z.O.SHENKAREV,E.I.FINKINA,E.K.NURMUKHAMEDOVA,S.V.BALANDIN, REMARK 1 AUTH 2 K.S.MINEEV,K.D.NADEZHDIN,Z.A.YAKIMENKO,A.A.TAGAEV, REMARK 1 AUTH 3 Y.V.TEMIROV,A.S.ARSENIEV,T.V.OVCHINNIKOVA REMARK 1 TITL ISOLATION, STRUCTURE ELUCIDATION, AND SYNERGISTIC REMARK 1 TITL 2 ANTIBACTERIAL ACTIVITY OF A NOVEL TWO-COMPONENT LANTIBIOTIC REMARK 1 TITL 3 LICHENICIDIN FROM BACILLUS LICHENIFORMIS VK21. REMARK 1 REF BIOCHEMISTRY V. 49 6462 2010 REMARK 1 REFN ISSN 1520-4995 REMARK 1 PMID 20578714 REMARK 1 DOI 10.1021/BI100871B REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 3.98.13 REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8C5J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-JAN-23. REMARK 100 THE DEPOSITION ID IS D_1292127831. 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 : 0 REMARK 210 PRESSURE : AMBIENT BAR REMARK 210 SAMPLE CONTENTS : 0.5 MM LCHA-1, METHANOL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H COSY; REMARK 210 2D 1H-1H TOCSY; 2D 1H-13C HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CARA 1.5, CYANA 3.98.13, TOPSPIN REMARK 210 2.1 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 400 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS 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: 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 1 ABA A 12 0.02 135.79 REMARK 500 1 CYS A 16 -85.19 -59.07 REMARK 500 1 LEU A 19 41.78 -94.18 REMARK 500 1 DAL A 20 -95.21 -49.35 REMARK 500 1 LYS A 21 54.13 34.46 REMARK 500 1 LEU A 23 -163.59 -115.95 REMARK 500 1 ASN A 26 175.47 51.42 REMARK 500 1 TYR A 28 -169.05 -113.44 REMARK 500 1 ABA A 31 15.44 44.10 REMARK 500 1 ABA A 33 178.99 62.20 REMARK 500 1 LYS A 34 -18.47 -45.22 REMARK 500 1 SER A 39 56.31 -142.46 REMARK 500 1 CYS A 40 -174.74 -55.83 REMARK 500 2 ABA A 12 -0.31 133.94 REMARK 500 2 CYS A 16 -85.21 -58.78 REMARK 500 2 LEU A 19 39.34 -88.59 REMARK 500 2 DAL A 20 -170.05 -54.55 REMARK 500 2 LYS A 21 70.23 35.00 REMARK 500 2 PRO A 22 -179.58 -69.72 REMARK 500 2 ABA A 31 3.15 51.98 REMARK 500 2 ABA A 33 174.40 63.39 REMARK 500 2 LYS A 34 -15.70 -47.27 REMARK 500 2 CYS A 40 102.19 -44.66 REMARK 500 3 ABA A 12 3.75 137.37 REMARK 500 3 LEU A 19 39.19 -95.16 REMARK 500 3 PRO A 22 -92.17 -69.77 REMARK 500 3 LEU A 23 179.01 -59.37 REMARK 500 3 ASN A 25 109.32 -45.52 REMARK 500 3 ASN A 26 161.97 -47.30 REMARK 500 3 TYR A 28 -164.98 -74.54 REMARK 500 3 LEU A 29 75.86 -60.06 REMARK 500 3 ABA A 31 16.88 44.11 REMARK 500 3 ABA A 33 -175.01 63.67 REMARK 500 3 LYS A 34 -9.93 -55.40 REMARK 500 3 CYS A 40 107.75 -41.97 REMARK 500 4 ILE A 11 87.34 -64.68 REMARK 500 4 ABA A 12 9.98 133.37 REMARK 500 4 LEU A 19 39.15 -87.99 REMARK 500 4 LYS A 21 156.25 172.85 REMARK 500 4 PRO A 22 -168.06 -69.81 REMARK 500 4 LEU A 23 -173.44 -57.80 REMARK 500 4 TYR A 28 -162.78 -63.64 REMARK 500 4 ABA A 31 3.52 51.88 REMARK 500 4 ABA A 33 174.03 64.50 REMARK 500 4 LYS A 34 -19.14 -45.01 REMARK 500 4 SER A 39 56.01 -143.18 REMARK 500 4 CYS A 40 -171.73 -57.77 REMARK 500 5 ABA A 12 11.38 135.49 REMARK 500 5 DAL A 20 -171.65 -65.69 REMARK 500 5 PRO A 22 -163.78 -69.73 REMARK 500 REMARK 500 THIS ENTRY HAS 222 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ILE A 11 ABA A 12 1 135.50 REMARK 500 CYS A 30 ABA A 31 1 135.64 REMARK 500 VAL A 32 ABA A 33 1 135.62 REMARK 500 ILE A 11 ABA A 12 2 135.61 REMARK 500 CYS A 30 ABA A 31 2 135.66 REMARK 500 VAL A 32 ABA A 33 2 135.55 REMARK 500 ILE A 11 ABA A 12 3 135.56 REMARK 500 CYS A 30 ABA A 31 3 135.58 REMARK 500 VAL A 32 ABA A 33 3 135.59 REMARK 500 ILE A 11 ABA A 12 4 135.56 REMARK 500 CYS A 30 ABA A 31 4 135.64 REMARK 500 VAL A 32 ABA A 33 4 135.56 REMARK 500 ILE A 11 ABA A 12 5 135.55 REMARK 500 CYS A 30 ABA A 31 5 135.60 REMARK 500 VAL A 32 ABA A 33 5 135.61 REMARK 500 ILE A 11 ABA A 12 6 135.51 REMARK 500 CYS A 30 ABA A 31 6 135.62 REMARK 500 VAL A 32 ABA A 33 6 135.60 REMARK 500 ILE A 11 ABA A 12 7 135.50 REMARK 500 CYS A 30 ABA A 31 7 135.58 REMARK 500 VAL A 32 ABA A 33 7 135.63 REMARK 500 ILE A 11 ABA A 12 8 135.53 REMARK 500 CYS A 30 ABA A 31 8 135.57 REMARK 500 VAL A 32 ABA A 33 8 135.56 REMARK 500 ILE A 11 ABA A 12 9 135.50 REMARK 500 CYS A 30 ABA A 31 9 135.61 REMARK 500 VAL A 32 ABA A 33 9 135.60 REMARK 500 ILE A 11 ABA A 12 10 135.53 REMARK 500 CYS A 30 ABA A 31 10 135.56 REMARK 500 VAL A 32 ABA A 33 10 135.59 REMARK 500 ILE A 11 ABA A 12 11 135.53 REMARK 500 CYS A 30 ABA A 31 11 135.60 REMARK 500 VAL A 32 ABA A 33 11 135.62 REMARK 500 ILE A 11 ABA A 12 12 135.54 REMARK 500 CYS A 30 ABA A 31 12 135.65 REMARK 500 VAL A 32 ABA A 33 12 135.62 REMARK 500 ILE A 11 ABA A 12 13 135.51 REMARK 500 CYS A 30 ABA A 31 13 135.62 REMARK 500 VAL A 32 ABA A 33 13 135.59 REMARK 500 ILE A 11 ABA A 12 14 135.56 REMARK 500 CYS A 30 ABA A 31 14 135.64 REMARK 500 VAL A 32 ABA A 33 14 135.59 REMARK 500 ILE A 11 ABA A 12 15 135.52 REMARK 500 CYS A 30 ABA A 31 15 135.57 REMARK 500 VAL A 32 ABA A 33 15 135.57 REMARK 500 ILE A 11 ABA A 12 16 135.50 REMARK 500 CYS A 30 ABA A 31 16 135.62 REMARK 500 VAL A 32 ABA A 33 16 135.59 REMARK 500 ILE A 11 ABA A 12 17 135.57 REMARK 500 CYS A 30 ABA A 31 17 135.57 REMARK 500 REMARK 500 THIS ENTRY HAS 60 NON CIS, NON-TRANS OMEGA OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 16709 RELATED DB: BMRB REMARK 900 RELATED ID: 2KTO RELATED DB: PDB REMARK 900 RELATED ID: 16707 RELATED DB: BMRB DBREF 8C5J A 10 41 UNP P86475 LANLA_BACLI 43 74 SEQADV 8C5J 2KT A 10 UNP P86475 THR 43 CONFLICT SEQADV 8C5J ABA A 12 UNP P86475 THR 45 CONFLICT SEQADV 8C5J DAL A 20 UNP P86475 SER 53 CONFLICT SEQADV 8C5J ABA A 31 UNP P86475 THR 64 CONFLICT SEQADV 8C5J ABA A 33 UNP P86475 THR 66 CONFLICT SEQRES 1 A 32 2KT ILE ABA LEU DHA DBU CYS ALA ILE LEU DAL LYS PRO SEQRES 2 A 32 LEU GLY ASN ASN GLY TYR LEU CYS ABA VAL ABA LYS GLU SEQRES 3 A 32 CYS MET PRO SER CYS ASN MODRES 8C5J DHA A 14 SER MODIFIED RESIDUE MODRES 8C5J DBU A 15 THR MODIFIED RESIDUE HET 2KT A 10 11 HET ABA A 12 12 HET DHA A 14 8 HET DBU A 15 11 HET DAL A 20 9 HET ABA A 31 12 HET ABA A 33 12 HETNAM 2KT 2-KETOBUTYRIC ACID HETNAM ABA ALPHA-AMINOBUTYRIC ACID HETNAM DHA 2-AMINO-ACRYLIC ACID HETNAM DBU (2Z)-2-AMINOBUT-2-ENOIC ACID HETNAM DAL D-ALANINE HETSYN 2KT 2-OXOBUTANOIC ACID HETSYN DHA 2,3-DIDEHYDROALANINE HETSYN DBU Z-DEHYDROBUTYRINE FORMUL 1 2KT C4 H6 O3 FORMUL 1 ABA 3(C4 H9 N O2) FORMUL 1 DHA C3 H5 N O2 FORMUL 1 DBU C4 H7 N O2 FORMUL 1 DAL C3 H7 N O2 HELIX 1 AA1 VAL A 32 MET A 37 1 6 LINK C 2KT A 10 N ILE A 11 1555 1555 1.33 LINK C ILE A 11 N ABA A 12 1555 1555 1.32 LINK C ABA A 12 N LEU A 13 1555 1555 1.33 LINK CB ABA A 12 SG CYS A 16 1555 1555 1.84 LINK C LEU A 13 N DHA A 14 1555 1555 1.33 LINK C DHA A 14 N DBU A 15 1555 1555 1.33 LINK C DBU A 15 N CYS A 16 1555 1555 1.33 LINK C LEU A 19 N DAL A 20 1555 1555 1.32 LINK C DAL A 20 N LYS A 21 1555 1555 1.33 LINK CB DAL A 20 SG CYS A 30 1555 1555 1.81 LINK C CYS A 30 N ABA A 31 1555 1555 1.32 LINK C ABA A 31 N VAL A 32 1555 1555 1.33 LINK CB ABA A 31 SG CYS A 36 1555 1555 1.85 LINK C VAL A 32 N ABA A 33 1555 1555 1.32 LINK C ABA A 33 N LYS A 34 1555 1555 1.33 LINK CB ABA A 33 SG CYS A 40 1555 1555 1.86 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 HETATM 1 C4 2KT A 10 0.750 0.500 -0.433 1.00 0.00 C HETATM 2 C3 2KT A 10 0.750 1.789 -0.433 1.00 0.00 C HETATM 3 C2 2KT A 10 1.898 2.311 -0.607 1.00 0.00 C HETATM 4 O3 2KT A 10 2.763 2.268 0.271 1.00 0.00 O HETATM 5 C 2KT A 10 2.187 2.924 -1.762 1.00 0.00 C HETATM 6 O 2KT A 10 1.311 2.969 -2.627 1.00 0.00 O HETATM 7 H41 2KT A 10 0.000 0.000 0.000 1.00 0.00 H HETATM 8 H42 2KT A 10 0.750 0.000 -1.299 1.00 0.00 H HETATM 9 H43 2KT A 10 1.500 0.000 0.000 1.00 0.00 H HETATM 10 H31 2KT A 10 0.039 1.903 -1.127 1.00 0.00 H HETATM 11 H32 2KT A 10 0.197 2.051 0.358 1.00 0.00 H