HEADER UNKNOWN FUNCTION 08-FEB-24 8VYC TITLE GRASPETIDE PRE-FUSCIMIDITIDE A1C/T3C VARIANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: ATP-GRASP TARGET RIPP; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOBIFIDA FUSCA YX; SOURCE 3 ORGANISM_TAXID: 269800; SOURCE 4 GENE: TFU_1807; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS GRASPETIDE, OMEGA-ESTER PEPTIDE, RIPP, CYCLIC PEPTIDE, UNKNOWN KEYWDS 2 FUNCTION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR A.J.LINK,B.CHOI REVDAT 2 15-MAY-24 8VYC 1 JRNL REVDAT 1 08-MAY-24 8VYC 0 JRNL AUTH B.CHOI,A.ACUNA,A.J.LINK JRNL TITL CYCLIC PEPTIDES FROM GRASPETIDE BIOSYNTHESIS AND NATIVE JRNL TITL 2 CHEMICAL LIGATION. JRNL REF J.AM.CHEM.SOC. V. 146 11605 2024 JRNL REFN ESSN 1520-5126 JRNL PMID 38634647 JRNL DOI 10.1021/JACS.4C02745 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 2.1 REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8VYC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-FEB-24. REMARK 100 THE DEPOSITION ID IS D_1000281415. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : 0 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 8.4 MM PRE-FUSCIMIDITIDE REMARK 210 A1C/T3C, 98% H2O/2% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H TOCSY; 2D 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : MESTRELAB (MNOVA / MESTRENOVA / REMARK 210 MESTREC), CYANA 2.1 REMARK 210 METHOD USED : DISTANCE GEOMETRY REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 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 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 1-20 REMARK 470 RES CSSEQI ATOMS REMARK 470 ASP A 18 OD2 REMARK 470 ASP A 22 OD2 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 OG1 THR A 7 CG ASP A 18 1.35 REMARK 500 N CYS A 1 CG ASP A 22 1.37 REMARK 500 OE2 GLU A 20 H ASP A 22 1.54 REMARK 500 OD2 ASP A 10 H VAL A 19 1.57 REMARK 500 HZ3 LYS A 13 OE1 GLN A 16 1.59 REMARK 500 REMARK 500 REMARK: NULL 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 ASP A 22 CB - CG - OD1 ANGL. DEV. = 6.5 DEGREES REMARK 500 1 ASP A 22 CA - C - O ANGL. DEV. = 56.2 DEGREES REMARK 500 2 ASP A 22 CA - C - O ANGL. DEV. = 58.4 DEGREES REMARK 500 3 ASP A 18 CB - CG - OD1 ANGL. DEV. = 6.8 DEGREES REMARK 500 3 ASP A 22 CA - C - O ANGL. DEV. = 53.9 DEGREES REMARK 500 4 ASP A 18 CB - CG - OD1 ANGL. DEV. = 7.0 DEGREES REMARK 500 4 ASP A 22 CA - C - O ANGL. DEV. = 57.9 DEGREES REMARK 500 5 ASP A 22 CA - C - O ANGL. DEV. = 56.3 DEGREES REMARK 500 6 ASP A 18 CB - CG - OD1 ANGL. DEV. = 6.9 DEGREES REMARK 500 6 ASP A 22 CA - C - O ANGL. DEV. = 57.6 DEGREES REMARK 500 7 ASP A 22 CA - C - O ANGL. DEV. = 57.3 DEGREES REMARK 500 8 ASP A 22 CA - C - O ANGL. DEV. = 57.9 DEGREES REMARK 500 9 ASP A 18 CB - CG - OD1 ANGL. DEV. = 6.4 DEGREES REMARK 500 9 ASP A 22 CB - CG - OD1 ANGL. DEV. = 6.0 DEGREES REMARK 500 9 ASP A 22 CA - C - O ANGL. DEV. = 57.8 DEGREES REMARK 500 10 ARG A 5 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 10 ASP A 18 CB - CG - OD1 ANGL. DEV. = 6.4 DEGREES REMARK 500 10 ASP A 22 CA - C - O ANGL. DEV. = 56.9 DEGREES REMARK 500 11 ASP A 22 CA - C - O ANGL. DEV. = 59.0 DEGREES REMARK 500 12 ASP A 22 CA - C - O ANGL. DEV. = 55.7 DEGREES REMARK 500 13 ASP A 18 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 13 ASP A 22 CA - C - O ANGL. DEV. = 57.6 DEGREES REMARK 500 14 ARG A 5 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 14 ASP A 22 CA - C - O ANGL. DEV. = 57.6 DEGREES REMARK 500 15 ASP A 22 CA - C - O ANGL. DEV. = 57.2 DEGREES REMARK 500 16 ASP A 22 CA - C - O ANGL. DEV. = 58.4 DEGREES REMARK 500 17 ASP A 22 CA - C - O ANGL. DEV. = 59.0 DEGREES REMARK 500 18 ASP A 18 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 18 ASP A 22 CA - C - O ANGL. DEV. = 56.7 DEGREES REMARK 500 19 ASP A 18 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 19 ASP A 22 CA - C - O ANGL. DEV. = 55.6 DEGREES REMARK 500 20 ASP A 18 CB - CG - OD1 ANGL. DEV. = 7.3 DEGREES REMARK 500 20 ASP A 22 CB - CG - OD1 ANGL. DEV. = 5.4 DEGREES REMARK 500 20 ASP A 22 CA - C - O ANGL. DEV. = 59.4 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 ARG A 5 80.03 -152.61 REMARK 500 1 GLN A 12 -43.44 -154.92 REMARK 500 1 LYS A 13 61.32 -162.09 REMARK 500 1 GLU A 20 168.23 178.81 REMARK 500 2 ARG A 5 41.44 85.66 REMARK 500 2 TYR A 8 93.34 -161.47 REMARK 500 2 ASP A 10 -147.43 -82.67 REMARK 500 2 GLN A 12 31.14 -82.65 REMARK 500 2 VAL A 19 26.20 -143.22 REMARK 500 3 LYS A 13 53.62 -140.83 REMARK 500 3 VAL A 19 -55.12 -126.63 REMARK 500 4 ASP A 10 -169.89 -78.83 REMARK 500 4 LYS A 13 71.74 48.80 REMARK 500 4 LYS A 21 36.31 -60.39 REMARK 500 5 CYS A 3 34.31 -168.65 REMARK 500 5 ARG A 5 55.64 -142.22 REMARK 500 5 VAL A 6 98.78 -66.69 REMARK 500 5 TYR A 8 55.07 -174.05 REMARK 500 5 PRO A 9 -75.13 -67.53 REMARK 500 5 LYS A 13 64.65 -167.73 REMARK 500 5 ASP A 18 -179.44 -176.91 REMARK 500 5 LYS A 21 176.84 160.35 REMARK 500 6 CYS A 3 -4.47 79.03 REMARK 500 6 LYS A 13 111.03 98.54 REMARK 500 6 VAL A 19 40.67 -80.09 REMARK 500 7 MET A 4 47.75 -81.51 REMARK 500 7 ASP A 10 33.87 -79.50 REMARK 500 7 GLN A 12 38.18 70.39 REMARK 500 7 PRO A 14 38.67 -78.69 REMARK 500 8 MET A 4 44.58 -151.85 REMARK 500 8 THR A 7 -166.09 -113.31 REMARK 500 8 GLN A 12 -71.65 -149.60 REMARK 500 8 LYS A 21 -178.29 172.51 REMARK 500 9 CYS A 3 63.90 68.44 REMARK 500 9 ASP A 10 48.58 -82.57 REMARK 500 10 GLN A 12 -55.87 -179.54 REMARK 500 10 LYS A 13 46.61 -161.65 REMARK 500 10 ASP A 18 140.30 -170.08 REMARK 500 11 ASP A 10 -153.04 -153.89 REMARK 500 11 GLN A 12 40.42 -163.43 REMARK 500 11 LYS A 13 71.44 -168.92 REMARK 500 11 VAL A 19 45.77 -80.53 REMARK 500 11 LYS A 21 66.65 -109.57 REMARK 500 12 MET A 4 41.33 -153.73 REMARK 500 12 ASP A 10 48.79 -82.00 REMARK 500 12 GLN A 12 42.53 -80.87 REMARK 500 12 GLN A 16 94.01 -64.89 REMARK 500 12 GLU A 20 44.09 -74.69 REMARK 500 13 ASP A 10 18.61 -65.66 REMARK 500 13 LYS A 13 60.19 71.92 REMARK 500 REMARK 500 THIS ENTRY HAS 74 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 GLN A 16 SER A 17 1 141.29 REMARK 500 ASP A 10 GLY A 11 3 141.49 REMARK 500 VAL A 19 GLU A 20 5 -141.49 REMARK 500 CYS A 1 GLY A 2 7 -149.37 REMARK 500 ARG A 5 VAL A 6 10 144.64 REMARK 500 PRO A 9 ASP A 10 11 -145.82 REMARK 500 ARG A 5 VAL A 6 14 135.86 REMARK 500 GLU A 20 LYS A 21 16 -104.87 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 TYR A 8 0.07 SIDE CHAIN REMARK 500 11 TYR A 8 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 31145 RELATED DB: BMRB REMARK 900 GRASPETIDE PRE-FUSCIMIDITIDE A1C/T3C VARIANT DBREF 8VYC A 1 22 UNP Q47NX9 Q47NX9_THEFY 68 89 SEQADV 8VYC CYS A 1 UNP Q47NX9 ALA 68 VARIANT SEQADV 8VYC CYS A 3 UNP Q47NX9 THR 70 VARIANT SEQRES 1 A 22 CYS GLY CYS MET ARG VAL THR TYR PRO ASP GLY GLN LYS SEQRES 2 A 22 PRO GLY GLN SER ASP VAL GLU LYS ASP 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