HEADER PEPTIDE BINDING PROTEIN 06-NOV-17 6EWT TITLE SOLUTION STRUCTURE OF RHABDOPEPTIDE NRPS DOCKING DOMAIN KJ12B-NDD COMPND MOL_ID: 1; COMPND 2 MOLECULE: NRPS KJ12B-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 5 19-JUN-24 6EWT 1 REMARK REVDAT 4 14-JUN-23 6EWT 1 REMARK REVDAT 3 23-JUN-21 6EWT 1 REMARK REVDAT 2 08-MAY-19 6EWT 1 REMARK REVDAT 1 31-OCT-18 6EWT 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 : OPALP 3.97 REMARK 3 AUTHORS : GUENTHERT REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6EWT 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_1200007312. 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 BAR REMARK 210 SAMPLE CONTENTS : 1 MM [U-13C; U-15N] KJ12BCDD, REMARK 210 90% H2O/10% D2O; 200 UM [U-15N] REMARK 210 KJ12BCDD, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HNCACB; 3D HNCO; 3D HN(CA)CO; REMARK 210 3D H(CCO)NH; 3D C(CO)NH; 3D REMARK 210 HBHA(CO)NH; 3D HCCH-TOCSY; 2D 1H- REMARK 210 15N HSQC; 3D 1H-15N NOESY-HSQC; REMARK 210 3D 1H-13C NOESY; 2D 1H-13C HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CARA 3.97, CCPNMR ANALYSIS, REMARK 210 TOPSPIN, CANDID, CYANA 3.97 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: 4670 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: 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: 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 SER A 62 C SER A 62 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 SER A 62 CA - C - O ANGL. DEV. = 41.0 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 2 SER A 33 44.98 -91.09 REMARK 500 3 SER A 33 42.90 -80.89 REMARK 500 4 SER A 33 43.08 -82.64 REMARK 500 6 SER A 33 22.81 -75.25 REMARK 500 7 THR A 29 -168.73 -172.78 REMARK 500 7 SER A 33 42.79 -87.57 REMARK 500 8 SER A 33 35.02 -72.72 REMARK 500 8 GLU A 60 -72.71 -89.67 REMARK 500 9 LYS A 2 108.23 -59.75 REMARK 500 9 THR A 29 -178.14 -175.35 REMARK 500 9 GLU A 60 10.53 -64.58 REMARK 500 11 SER A 33 28.97 -70.19 REMARK 500 13 THR A 29 -179.96 -174.15 REMARK 500 14 SER A 33 31.41 -86.09 REMARK 500 15 SER A 33 22.33 -76.24 REMARK 500 16 SER A 33 42.16 -86.85 REMARK 500 17 SER A 33 52.90 -91.01 REMARK 500 18 THR A 29 146.69 -177.81 REMARK 500 18 SER A 33 56.72 -94.83 REMARK 500 18 GLU A 60 -29.39 -167.90 REMARK 500 19 THR A 29 147.98 176.39 REMARK 500 19 SER A 33 40.34 -82.85 REMARK 500 19 GLU A 60 -67.03 -102.75 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 8 ARG A 31 0.07 SIDE CHAIN REMARK 500 15 TYR A 27 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34194 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF RHABDOPEPTIDE NRPS DOCKING DOMAIN KJ12DD DBREF1 6EWT A 1 62 UNP A0A173DW12_9GAMM DBREF2 6EWT A A0A173DW12 1 62 SEQRES 1 A 62 MET LYS ASN ALA ALA LYS ILE VAL ASN GLU ALA LEU ASN SEQRES 2 A 62 GLN GLY ILE THR LEU PHE VAL SER ASP ASN LYS LEU LYS SEQRES 3 A 62 TYR LYS THR ASN ARG ASP SER ILE PRO SER GLU LEU LEU SEQRES 4 A 62 GLU GLU TRP LYS GLN HIS LYS GLN GLU LEU ILE ASP PHE SEQRES 5 A 62 LEU THR GLN LEU GLU SER GLU GLU GLU SER HELIX 1 AA1 ASN A 3 GLN A 14 1 12 HELIX 2 AA2 PRO A 35 HIS A 45 1 11 HELIX 3 AA3 HIS A 45 SER A 58 1 14 SHEET 1 AA1 2 ILE A 16 VAL A 20 0 SHEET 2 AA1 2 LEU A 25 THR A 29 -1 O LYS 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