HEADER PEPTIDE BINDING PROTEIN 06-NOV-17 6EWS TITLE SOLUTION STRUCTURE OF RHABDOPEPTIDE NRPS DOCKING DOMAIN KJ12A-NDD COMPND MOL_ID: 1; COMPND 2 MOLECULE: NRPS KJ12A-NDD; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: XENORHABDUS STOCKIAE; SOURCE 3 ORGANISM_TAXID: 351614; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS PROTEIN, PEPTIDE BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR C.HACKER,X.CAI,C.KEGLER,L.ZHAO,A.K.WEICKHMANN,H.B.BODE,J.WOEHNERT REVDAT 4 14-JUN-23 6EWS 1 REMARK REVDAT 3 23-JUN-21 6EWS 1 REMARK REVDAT 2 08-MAY-19 6EWS 1 REMARK REVDAT 1 31-OCT-18 6EWS 0 JRNL AUTH C.HACKER,X.CAI,C.KEGLER,L.ZHAO,A.K.WEICKHMANN,J.P.WURM, JRNL AUTH 2 H.B.BODE,J.WOHNERT JRNL TITL STRUCTURE-BASED REDESIGN OF DOCKING DOMAIN INTERACTIONS JRNL TITL 2 MODULATES THE PRODUCT SPECTRUM OF A JRNL TITL 3 RHABDOPEPTIDE-SYNTHESIZING NRPS. JRNL REF NAT COMMUN V. 9 4366 2018 JRNL REFN ESSN 2041-1723 JRNL PMID 30341296 JRNL DOI 10.1038/S41467-018-06712-1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 3.97, OPALP REMARK 3 AUTHORS : GUENTERT (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6EWS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-NOV-17. REMARK 100 THE DEPOSITION ID IS D_1200007311. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : AMBIENT PA REMARK 210 SAMPLE CONTENTS : 1 MM [U-13C; U-15N] KJ12A NDD, REMARK 210 90% H2O/10% D2O; 500 UM [U-15N] REMARK 210 KJ12A NDD, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCACB; 3D REMARK 210 HNCO; 3D HN(CA)CO; 3D HCCH-TOCSY; REMARK 210 3D 1H-15N NOESY; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 2D 1H-13C HSQC REMARK 210 AROMATIC; 3D 1H-13C NOESY REMARK 210 AROMATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ; 950 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN 3.97, CARA, CCPNMR REMARK 210 ANALYSIS, CANDID REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5000 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 2 GLN A 63 C GLN A 63 O 0.771 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 2 GLN A 63 CA - C - O ANGL. DEV. = 41.1 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 ALA A 58 51.33 37.39 REMARK 500 3 ASN A 23 19.80 57.37 REMARK 500 3 SER A 30 20.64 -145.49 REMARK 500 3 ASN A 33 152.10 178.39 REMARK 500 3 ALA A 58 16.68 58.78 REMARK 500 5 ASN A 23 19.74 59.98 REMARK 500 7 ASP A 22 19.72 55.50 REMARK 500 8 ALA A 58 13.21 50.42 REMARK 500 9 GLU A 61 2.47 -152.26 REMARK 500 10 TYR A 44 -70.90 -64.51 REMARK 500 10 TYR A 45 24.39 -79.09 REMARK 500 11 LEU A 49 -71.14 -60.68 REMARK 500 12 LEU A 49 -72.68 -57.55 REMARK 500 12 GLU A 60 103.47 -58.51 REMARK 500 14 ASN A 23 19.71 55.44 REMARK 500 15 ALA A 58 17.87 52.82 REMARK 500 17 ASN A 23 18.98 57.68 REMARK 500 17 ALA A 58 16.29 58.71 REMARK 500 18 GLU A 61 -176.64 -177.94 REMARK 500 19 ASN A 33 -168.07 -161.00 REMARK 500 19 LEU A 49 -71.94 -54.98 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 6 TYR A 27 0.07 SIDE CHAIN REMARK 500 7 TYR A 45 0.08 SIDE CHAIN REMARK 500 8 ARG A 24 0.08 SIDE CHAIN REMARK 500 11 TYR A 27 0.09 SIDE CHAIN REMARK 500 11 ARG A 31 0.08 SIDE CHAIN REMARK 500 12 TYR A 27 0.08 SIDE CHAIN REMARK 500 14 TYR A 44 0.07 SIDE CHAIN REMARK 500 15 TYR A 27 0.09 SIDE CHAIN REMARK 500 18 ARG A 31 0.09 SIDE CHAIN REMARK 500 19 ARG A 46 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34193 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF RHABDOPEPTIDE NRPS DOCKING DOMAIN KJ12CDD DBREF1 6EWS A 1 63 UNP A0A173DW33_9GAMM DBREF2 6EWS A A0A173DW33 1 63 SEQRES 1 A 63 MET LYS ASN ALA ALA GLN ILE VAL ASP GLU ALA LEU ASN SEQRES 2 A 63 GLN GLY ILE THR LEU PHE VAL ALA ASP ASN ARG LEU GLN SEQRES 3 A 63 TYR GLU THR SER ARG ASP ASN ILE PRO GLU GLU LEU LEU SEQRES 4 A 63 ASN GLU TRP LYS TYR TYR ARG GLN ASP LEU ILE ASP PHE SEQRES 5 A 63 LEU GLN GLN LEU ASP ALA LYS GLU GLU THR GLN HELIX 1 AA1 ASN A 3 ASN A 13 1 11 HELIX 2 AA2 PRO A 35 TYR A 45 1 11 HELIX 3 AA3 TYR A 45 ALA A 58 1 14 SHEET 1 AA1 2 ILE A 16 ALA A 21 0 SHEET 2 AA1 2 ARG A 24 THR A 29 -1 O GLU A 28 N THR A 17 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