HEADER TRANSFERASE 26-JUL-22 8AIG TITLE NMR STRUCTURE OF HOLO-ACP COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYBRID NON RIBOSOMAL PEPTIDE SYNTHETASE-POLYKETIDE COMPND 3 SYNTHASE; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES VIRGINIAE; SOURCE 3 ORGANISM_TAXID: 1961; SOURCE 4 GENE: VIRG; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ACYL CARRIER PROTEIN, TRANSFERASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR S.COLLIN,K.J.WEISSMAN,B.CHAGOT,A.GRUEZ REVDAT 2 29-MAR-23 8AIG 1 JRNL REVDAT 1 22-MAR-23 8AIG 0 JRNL AUTH S.COLLIN,R.J.COX,C.PARIS,C.JACOB,B.CHAGOT,K.J.WEISSMAN, JRNL AUTH 2 A.GRUEZ JRNL TITL DECRYPTING THE PROGRAMMING OF BETA-METHYLATION IN JRNL TITL 2 VIRGINIAMYCIN M BIOSYNTHESIS. JRNL REF NAT COMMUN V. 14 1327 2023 JRNL REFN ESSN 2041-1723 JRNL PMID 36899003 JRNL DOI 10.1038/S41467-023-36974-3 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8AIG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-JUL-22. REMARK 100 THE DEPOSITION ID IS D_1292124354. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 0.1 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1.0 MM [U-100% 13C; U-100% 15N] REMARK 210 VIRGINIAMYCIN ACP6, 100 MM REMARK 210 SODIUM PHOSPHATE, 0.5 MM TCEP, REMARK 210 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 2D 1H-1H(C12,N14) NOESY; 2D REMARK 210 1H(C12,N14)-1H(C12,N14) NOESY; REMARK 210 3D HNCACB; 3D HNCO; 3D HCCH- REMARK 210 TOCSY; 3D CCH-TOCSY; 3D 1H-13C REMARK 210 NOESY; 3D 1H-15N NOESY; 3D 1H- REMARK 210 13C NOESY AROMATIC; 3D HNHA REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA, NMRFAM-SPARKY REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 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: 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 2 ARG A1129 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 3 ARG A1084 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 3 ARG A1085 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 3 ARG A1094 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 3 ARG A1129 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 4 ARG A1084 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 4 ARG A1129 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 5 ARG A1084 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 5 ARG A1085 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES REMARK 500 5 ARG A1129 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 6 ARG A1085 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 6 ARG A1094 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 6 ARG A1129 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 7 ARG A1085 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 7 ARG A1129 NE - CZ - NH2 ANGL. DEV. = 4.6 DEGREES REMARK 500 7 ARG A1146 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 8 ARG A1085 NE - CZ - NH1 ANGL. DEV. = 5.0 DEGREES REMARK 500 8 ARG A1124 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 8 ARG A1129 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 9 ARG A1085 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 10 ARG A1084 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 10 ARG A1085 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 10 ARG A1094 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 10 ARG A1129 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 11 ARG A1084 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 11 ARG A1085 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 11 ARG A1091 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 12 ARG A1085 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 12 ARG A1094 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 12 ARG A1129 NE - CZ - NH1 ANGL. DEV. = 4.6 DEGREES REMARK 500 13 ARG A1094 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 13 ARG A1129 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 13 ARG A1146 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 14 ARG A1085 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 14 ARG A1094 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 14 ARG A1129 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 14 ARG A1146 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 15 ARG A1085 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 15 ARG A1129 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 16 ARG A1129 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 17 ARG A1129 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 18 ARG A1091 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 19 ARG A1085 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 20 ARG A1084 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 20 ARG A1085 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 20 ARG A1091 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 20 ARG A1129 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 20 ARG A1146 NE - CZ - NH1 ANGL. DEV. = 3.3 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 VAL A1134 -74.53 -130.26 REMARK 500 2 GLU A1133 -39.15 -140.81 REMARK 500 2 VAL A1134 -71.92 -91.26 REMARK 500 3 VAL A1134 -74.18 -130.58 REMARK 500 4 ASP A1082 39.10 -82.57 REMARK 500 4 VAL A1134 -78.41 -134.73 REMARK 500 5 SER A1120 -60.03 -26.91 REMARK 500 5 VAL A1134 -72.62 -131.91 REMARK 500 6 ALA A1078 14.02 57.01 REMARK 500 6 VAL A1134 -71.99 -132.36 REMARK 500 7 SER A -1 -58.31 -152.26 REMARK 500 7 VAL A1134 -76.33 -134.39 REMARK 500 8 ASP A1081 33.09 -93.53 REMARK 500 8 VAL A1134 -77.75 -133.51 REMARK 500 9 ALA A1078 15.74 56.49 REMARK 500 9 GLU A1133 -37.08 -141.63 REMARK 500 9 VAL A1134 -66.40 -91.13 REMARK 500 10 VAL A1134 -73.74 -124.22 REMARK 500 11 ASP A1081 40.60 -75.98 REMARK 500 11 VAL A1134 -78.10 -105.08 REMARK 500 12 ALA A1079 9.09 60.00 REMARK 500 12 ASP A1082 14.37 54.50 REMARK 500 12 VAL A1134 -78.08 -126.93 REMARK 500 12 ARG A1146 -47.30 -134.47 REMARK 500 13 ASP A1082 34.34 -73.45 REMARK 500 13 VAL A1134 -73.32 -129.98 REMARK 500 14 VAL A1134 -68.45 -123.07 REMARK 500 15 ASP A1081 25.69 -150.85 REMARK 500 15 VAL A1134 -72.12 -133.35 REMARK 500 16 ALA A1079 -165.96 56.49 REMARK 500 16 VAL A1134 -74.79 -120.91 REMARK 500 17 VAL A1134 -70.93 -130.73 REMARK 500 18 VAL A1134 -73.82 -128.16 REMARK 500 19 GLU A1133 -5.81 -143.37 REMARK 500 19 VAL A1134 -75.92 -111.39 REMARK 500 19 ARG A1146 -43.55 -139.33 REMARK 500 20 VAL A1134 -65.90 -130.25 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 13 ARG A1146 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34743 RELATED DB: BMRB REMARK 900 NMR STRUCTURE OF HOLO-ACP DBREF 8AIG A 1078 1159 UNP A4PHM4 A4PHM4_STRVG 332 413 SEQADV 8AIG GLY A -4 UNP A4PHM4 EXPRESSION TAG SEQADV 8AIG PRO A -3 UNP A4PHM4 EXPRESSION TAG SEQADV 8AIG GLY A -2 UNP A4PHM4 EXPRESSION TAG SEQADV 8AIG SER A -1 UNP A4PHM4 EXPRESSION TAG SEQRES 1 A 86 GLY PRO GLY SER ALA ALA ALA ASP ASP GLY ARG ARG ALA SEQRES 2 A 86 GLU LEU ALA ASP ARG VAL SER ARG THR VAL ALA ASP THR SEQRES 3 A 86 ILE GLY ARG PRO ALA GLY SER ILE GLY GLY HIS THR SER SEQRES 4 A 86 LEU GLU SER MET GLY LEU ASP SER VAL MET ILE ARG ALA SEQRES 5 A 86 LEU ALA SER ARG LEU SER ALA GLU VAL ALA PRO VAL GLY SEQRES 6 A 86 PRO GLU MET LEU PHE GLY LEU ARG ASP LEU ASP GLU LEU SEQRES 7 A 86 VAL ASP HIS LEU VAL ALA ALA ARG HET PNS A1201 42 HETNAM PNS 4'-PHOSPHOPANTETHEINE FORMUL 2 PNS C11 H23 N2 O7 P S HELIX 1 AA1 ASP A 1081 GLY A 1101 1 21 HELIX 2 AA2 PRO A 1103 ILE A 1107 5 5 HELIX 3 AA3 ASP A 1119 VAL A 1134 1 16 HELIX 4 AA4 GLY A 1138 PHE A 1143 1 6 HELIX 5 AA5 ASP A 1147 ARG A 1159 1 13 LINK OG SER A1120 P24 PNS A1201 1555 1555 1.60 CISPEP 1 SER A -1 ALA A 1078 1 -6.10 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