HEADER PEPTIDE BINDING PROTEIN 06-NOV-17 6EWV TITLE SOLUTION STRUCTURE OF DOCKING DOMAIN COMPLEX OF RXP NRPS: KJ12C NDD - TITLE 2 KJ12B CDD COMPND MOL_ID: 1; COMPND 2 MOLECULE: NRPS KJ12C-NDD, NRPS KJ12B-CDD; 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-GOLD(DE3)PLYSS AG'; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 866768 KEYWDS PROTEIN, SOLUTION STRUCTURE, RHABDOPEPTIDE, DOCKING DOMAINS, PEPTIDE KEYWDS 2 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 6EWV 1 REMARK REVDAT 3 23-JUN-21 6EWV 1 REMARK REVDAT 2 08-MAY-19 6EWV 1 REMARK REVDAT 1 31-OCT-18 6EWV 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 : GUENTERT PETER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6EWV 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_1200006564. 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 : 150 REMARK 210 PRESSURE : AMBIENT PA REMARK 210 SAMPLE CONTENTS : 700 UM [U-99% 15N] KJ12C NDD REMARK 210 12XGS KJ12B CDD, 90% H2O/10% D2O; REMARK 210 850 UM [U-99% 13C; U-99% 15N] REMARK 210 KJ12C NDD 12XGS KJ12B CDD, 90% REMARK 210 H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-15N NOESY; 2D 1H-15N B-TR REMARK 210 -HSQC; 3D 1H-13C NOESY; 2D 1H- REMARK 210 13C HSQC ALIPHATIC; 2D 1H-13C REMARK 210 HSQC AROMATIC; 3D HCCH-TOCSY; 3D REMARK 210 HBHA(CO)NH; 3D B-TR-HNCO; 3D B- REMARK 210 TR-HNCACB; 3D B-TR-HN(CO)CA REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CARA 1.8.4.2, TOPSPIN 3.5, REMARK 210 CCPNMR ANALYSIS, UNIO 10, CYANA REMARK 210 3.97 REMARK 210 METHOD USED : MOLECULAR 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC 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: 7730 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 ILE A1568 C ILE A1568 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 1 ARG A 31 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 2 ILE A1568 CA - C - O ANGL. DEV. = 41.1 DEGREES REMARK 500 8 ARG A 24 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 9 ARG A 24 CD - NE - CZ ANGL. DEV. = 8.4 DEGREES REMARK 500 9 ARG A 24 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 9 ARG A 24 NE - CZ - NH2 ANGL. DEV. = -5.0 DEGREES REMARK 500 11 ARG A 24 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 13 ARG A 31 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 15 ARG A 24 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 15 ARG A 24 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 19 ARG A 24 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 20 ARG A 24 NE - CZ - NH2 ANGL. DEV. = -4.0 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 1 THR A 29 140.48 -176.87 REMARK 500 1 ARG A 31 -84.31 -120.49 REMARK 500 1 SER A 33 -161.64 156.65 REMARK 500 1 LYS A 63 -139.89 52.45 REMARK 500 1 GLN A1557 167.70 54.95 REMARK 500 1 SER A1559 83.09 42.72 REMARK 500 1 SER A1560 70.20 51.83 REMARK 500 2 PHE A 19 -177.81 -171.03 REMARK 500 2 THR A 29 130.40 -173.56 REMARK 500 2 SER A 30 73.62 -115.53 REMARK 500 2 ARG A 31 -88.79 -127.17 REMARK 500 2 SER A 33 -173.86 153.73 REMARK 500 2 GLN A 61 19.23 53.70 REMARK 500 2 LYS A 63 -150.20 179.78 REMARK 500 2 SER A 65 -160.50 -79.41 REMARK 500 2 SER A 73 -13.55 79.00 REMARK 500 2 SER A 75 114.10 61.64 REMARK 500 2 LEU A1545 -39.14 -36.39 REMARK 500 2 GLN A1554 86.15 -175.60 REMARK 500 2 ALA A1555 -116.95 133.34 REMARK 500 2 GLU A1556 -78.08 65.04 REMARK 500 2 GLN A1557 -2.28 73.98 REMARK 500 2 ASN A1558 -39.94 71.06 REMARK 500 2 SER A1559 21.44 49.10 REMARK 500 2 SER A1560 28.18 -163.96 REMARK 500 3 THR A 29 135.25 -176.78 REMARK 500 3 SER A 30 78.66 -112.16 REMARK 500 3 ARG A 31 -84.81 -120.73 REMARK 500 3 SER A 33 -157.39 157.75 REMARK 500 3 SER A 65 -167.75 86.38 REMARK 500 3 SER A 69 7.68 -161.08 REMARK 500 3 SER A 73 71.73 41.10 REMARK 500 3 SER A1559 17.98 48.75 REMARK 500 4 THR A 29 137.02 -178.68 REMARK 500 4 SER A 30 77.52 -112.80 REMARK 500 4 ARG A 31 -85.75 -122.98 REMARK 500 4 SER A 33 -150.86 160.05 REMARK 500 4 SER A 67 174.19 69.50 REMARK 500 4 ALA A1555 -139.21 -119.52 REMARK 500 5 ILE A 2 123.79 118.63 REMARK 500 5 ASN A 23 32.87 71.62 REMARK 500 5 THR A 29 138.60 -179.04 REMARK 500 5 ARG A 31 -83.22 -120.80 REMARK 500 5 SER A 33 -160.38 157.66 REMARK 500 5 GLN A 61 -17.13 62.20 REMARK 500 5 SER A 65 -6.50 -151.75 REMARK 500 6 THR A 29 139.77 -179.06 REMARK 500 6 ARG A 31 -84.66 -120.33 REMARK 500 6 SER A 33 -156.16 160.41 REMARK 500 6 SER A 71 -151.51 42.22 REMARK 500 REMARK 500 THIS ENTRY HAS 189 RAMACHANDRAN OUTLIERS. 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 ARG A 24 0.10 SIDE CHAIN REMARK 500 6 TYR A 27 0.08 SIDE CHAIN REMARK 500 6 TYR A1563 0.09 SIDE CHAIN REMARK 500 7 TYR A 27 0.08 SIDE CHAIN REMARK 500 7 TYR A1563 0.08 SIDE CHAIN REMARK 500 10 ARG A 24 0.09 SIDE CHAIN REMARK 500 11 ARG A 24 0.10 SIDE CHAIN REMARK 500 11 ARG A 31 0.09 SIDE CHAIN REMARK 500 16 TYR A1563 0.10 SIDE CHAIN REMARK 500 17 ARG A 24 0.10 SIDE CHAIN REMARK 500 19 ARG A 31 0.09 SIDE CHAIN REMARK 500 20 ARG A 24 0.14 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34196 RELATED DB: BMRB REMARK 900 RH3NDD RH2CDD COMPLEX STRUCTURE DBREF1 6EWV A 2 63 UNP A0A173DW42_9GAMM DBREF2 6EWV A A0A173DW42 2 63 DBREF1 6EWV A 1545 1568 UNP A0A173DW12_9GAMM DBREF2 6EWV A A0A173DW12 1545 1568 SEQADV 6EWV GLY A 1 UNP A0A173DW4 EXPRESSION TAG SEQADV 6EWV GLY A 64 UNP A0A173DW4 LINKER SEQADV 6EWV SER A 65 UNP A0A173DW4 LINKER SEQADV 6EWV GLY A 66 UNP A0A173DW4 LINKER SEQADV 6EWV SER A 67 UNP A0A173DW4 LINKER SEQADV 6EWV GLY A 68 UNP A0A173DW4 LINKER SEQADV 6EWV SER A 69 UNP A0A173DW4 LINKER SEQADV 6EWV GLY A 70 UNP A0A173DW4 LINKER SEQADV 6EWV SER A 71 UNP A0A173DW4 LINKER SEQADV 6EWV GLY A 72 UNP A0A173DW4 LINKER SEQADV 6EWV SER A 73 UNP A0A173DW4 LINKER SEQADV 6EWV GLY A 74 UNP A0A173DW4 LINKER SEQADV 6EWV SER A 75 UNP A0A173DW4 LINKER SEQRES 1 A 99 GLY ILE ASP ALA ALA GLN ILE VAL ASP GLU ALA LEU GLU SEQRES 2 A 99 GLN GLY ILE THR LEU PHE VAL VAL ASN ASN ARG LEU GLN SEQRES 3 A 99 TYR GLU THR SER ARG ASP SER ILE PRO THR GLU LEU LEU SEQRES 4 A 99 ASN LYS TRP LYS GLN HIS LYS GLN GLU LEU ILE ASP PHE SEQRES 5 A 99 LEU ASN GLN LEU ASP SER GLU GLU GLN THR LYS GLY SER SEQRES 6 A 99 GLY SER GLY SER GLY SER GLY SER GLY SER LEU LEU LYS SEQRES 7 A 99 GLU LYS ARG LYS HIS PHE GLN ALA GLU GLN ASN SER SER SEQRES 8 A 99 GLN GLU TYR LEU ARG GLY GLU ILE HELIX 1 AA1 ASP A 3 GLY A 15 1 13 HELIX 2 AA2 PRO A 35 HIS A 45 1 11 HELIX 3 AA3 HIS A 45 GLN A 61 1 17 HELIX 4 AA4 LEU A 1545 GLN A 1554 1 10 SHEET 1 AA1 3 THR A 17 VAL A 21 0 SHEET 2 AA1 3 ARG A 24 THR A 29 -1 O GLU A 28 N THR A 17 SHEET 3 AA1 3 LEU A1564 GLU A1567 -1 O GLY A1566 N TYR A 27 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