HEADER PROTEIN BINDING 19-DEC-19 6TRP TITLE SOLUTION STRUCTURE OF DOCKING DOMAIN COMPLEX OF PAX NRPS: PAXC NDD - TITLE 2 PAXB CDD COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDE SYNTHETASE XPSB,PEPTIDE SYNTHETASE XPSB; COMPND 3 CHAIN: A; COMPND 4 EC: 2.7.7.58,5.1.1.12,5.1.1.11,6.2.1.26; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: XENORHABDUS BOVIENII SS-2004; SOURCE 3 ORGANISM_TAXID: 406818; SOURCE 4 GENE: XBJ1_2151, XBJ1_2152; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS PROTEIN, NRPS, DOCKING DOMAINS, COMMUNICATION-MEDIATING DOMAINS, KEYWDS 2 PROTEIN BINDING EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.WATZEL,C.HACKER,E.DUCHARDT-FERNER,H.B.BODE,J.WOEHNERT REVDAT 3 14-JUN-23 6TRP 1 REMARK REVDAT 2 23-JUN-21 6TRP 1 REMARK REVDAT 1 12-AUG-20 6TRP 0 JRNL AUTH J.WATZEL,C.HACKER,E.DUCHARDT-FERNER,H.B.BODE,J.WOHNERT JRNL TITL A NEW DOCKING DOMAIN TYPE IN THE JRNL TITL 2 PEPTIDE-ANTIMICROBIAL-XENORHABDUS PEPTIDE PRODUCING JRNL TITL 3 NONRIBOSOMAL PEPTIDE SYNTHETASE FROMXENORHABDUS BOVIENII. JRNL REF ACS CHEM.BIOL. V. 15 982 2020 JRNL REFN ESSN 1554-8937 JRNL PMID 32167274 JRNL DOI 10.1021/ACSCHEMBIO.9B01022 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 3.97 REMARK 3 AUTHORS : GUENTERT, PETER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6TRP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-DEC-19. REMARK 100 THE DEPOSITION ID IS D_1292105159. 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 : 370 UM [U-99% 13C; U-99% 15N] REMARK 210 PAXC NDD 12.5XGS Y-PAXB CDD, 90% REMARK 210 H2O/10% D2O; 1620 UM [U-99% 13C; REMARK 210 U-99% 15N] PAXC NDD 12.5XGS Y- REMARK 210 PAXB CDD, 90% H2O/10% D2O; 730 REMARK 210 UM [U-99% 15N] PAXC NDD 12.5XGS REMARK 210 Y-PAXB CDD, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC, 3D B-TR-HNCACB, REMARK 210 3D B-TR-HNCO, 3D HC(C)H-TOCSY; REMARK 210 2D 1H-15N HSQC, 3D (H)CCH-TOCSY; REMARK 210 2D 1H-15N HSQC, 3D HBHA(CO)NH, REMARK 210 3D HN(CA)CO, 3D H(CCO)NH; 2D 1H- REMARK 210 15N HSQC, 3D 1H-15N NOESY; 2D 1H- REMARK 210 13C HSQC ALIPHATIC, 3D 1H-13C REMARK 210 NOESY ALIPHATIC; 2D 1H-13C HSQC REMARK 210 AROMATIC, 3D 1H-13C NOESY REMARK 210 AROMATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 700 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 2.4.2, UNIO 10, REMARK 210 CYANA REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 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: 8260 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 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 14 ARG A 23 NE - CZ - NH1 ANGL. DEV. = 3.1 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 ILE A 3 151.54 -39.91 REMARK 500 1 SER A 27 19.78 51.29 REMARK 500 1 SER A 29 -64.11 -127.32 REMARK 500 1 SER A 35 -30.17 -160.28 REMARK 500 1 TYR A 59 -137.07 -77.80 REMARK 500 1 PHE A3292 -43.52 -164.64 REMARK 500 1 PHE A3293 12.35 -142.34 REMARK 500 2 THR A 30 30.34 -141.07 REMARK 500 2 TYR A 33 -68.12 -128.32 REMARK 500 2 SER A 35 -99.81 -151.96 REMARK 500 2 SER A 39 -1.16 57.48 REMARK 500 2 PHE A3292 -56.32 -153.58 REMARK 500 3 THR A 30 43.11 -162.94 REMARK 500 3 SER A 47 -12.45 -149.72 REMARK 500 3 TYR A 59 -178.69 -68.15 REMARK 500 3 PHE A3292 -59.81 -153.15 REMARK 500 3 GLN A3320 87.26 -163.96 REMARK 500 4 SER A 27 -33.20 70.35 REMARK 500 4 THR A 30 29.71 -165.29 REMARK 500 4 LYS A 32 38.78 -67.11 REMARK 500 4 TYR A 33 -74.54 -64.61 REMARK 500 4 SER A 39 -115.37 -81.68 REMARK 500 4 SER A 57 -96.88 -148.29 REMARK 500 4 PHE A3292 -47.89 -162.59 REMARK 500 4 ASP A3319 -149.50 -138.59 REMARK 500 4 GLN A3320 27.01 -141.43 REMARK 500 5 SER A 27 2.00 56.21 REMARK 500 5 SER A 29 -51.34 -131.90 REMARK 500 5 THR A 30 37.83 -150.91 REMARK 500 5 LYS A 32 -74.74 -36.96 REMARK 500 5 SER A 39 -130.50 -105.16 REMARK 500 5 SER A 41 7.69 56.00 REMARK 500 5 SER A 45 79.57 -158.18 REMARK 500 5 TYR A 59 -177.90 -63.19 REMARK 500 5 PHE A3292 -53.48 -162.57 REMARK 500 5 ASP A3319 -157.85 -136.52 REMARK 500 5 GLN A3320 35.18 -143.54 REMARK 500 6 ASN A 2 92.95 -65.51 REMARK 500 6 SER A 27 29.53 48.86 REMARK 500 6 SER A 29 -53.92 -126.70 REMARK 500 6 LYS A 32 -73.49 -21.70 REMARK 500 6 TYR A 33 44.65 -148.84 REMARK 500 6 SER A 35 -62.69 -124.77 REMARK 500 6 SER A 37 -77.48 -73.59 REMARK 500 6 SER A 41 -167.02 -103.17 REMARK 500 6 SER A 49 -78.18 -139.67 REMARK 500 6 SER A 55 170.31 77.94 REMARK 500 6 TYR A 59 -168.97 -67.65 REMARK 500 6 PHE A3292 -85.19 -144.62 REMARK 500 7 ASN A 4 -48.25 -140.56 REMARK 500 REMARK 500 THIS ENTRY HAS 156 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 2 ARG A 12 0.09 SIDE CHAIN REMARK 500 3 ARG A 12 0.13 SIDE CHAIN REMARK 500 4 TYR A 59 0.09 SIDE CHAIN REMARK 500 9 TYR A 33 0.07 SIDE CHAIN REMARK 500 12 ARG A 23 0.14 SIDE CHAIN REMARK 500 17 ARG A 12 0.08 SIDE CHAIN REMARK 500 19 ARG A 23 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34469 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF DOCKING DOMAIN COMPLEX OF PAX NRPS: PAXC NDD - REMARK 900 PAXB CDD DBREF 6TRP A 1 33 UNP D3V3G2 D3V3G2_XENBS 1 33 DBREF 6TRP A 3288 3321 UNP D3V3G3 D3V3G3_XENBS 3288 3321 SEQADV 6TRP GLY A 34 UNP D3V3G2 LINKER SEQADV 6TRP SER A 35 UNP D3V3G2 LINKER SEQADV 6TRP GLY A 36 UNP D3V3G2 LINKER SEQADV 6TRP SER A 37 UNP D3V3G2 LINKER SEQADV 6TRP GLY A 38 UNP D3V3G2 LINKER SEQADV 6TRP SER A 39 UNP D3V3G2 LINKER SEQADV 6TRP GLY A 40 UNP D3V3G2 LINKER SEQADV 6TRP SER A 41 UNP D3V3G2 LINKER SEQADV 6TRP GLY A 42 UNP D3V3G2 LINKER SEQADV 6TRP SER A 43 UNP D3V3G2 LINKER SEQADV 6TRP GLY A 44 UNP D3V3G2 LINKER SEQADV 6TRP SER A 45 UNP D3V3G2 LINKER SEQADV 6TRP GLY A 46 UNP D3V3G2 LINKER SEQADV 6TRP SER A 47 UNP D3V3G2 LINKER SEQADV 6TRP GLY A 48 UNP D3V3G2 LINKER SEQADV 6TRP SER A 49 UNP D3V3G2 LINKER SEQADV 6TRP GLY A 50 UNP D3V3G2 LINKER SEQADV 6TRP SER A 51 UNP D3V3G2 LINKER SEQADV 6TRP GLY A 52 UNP D3V3G2 LINKER SEQADV 6TRP SER A 53 UNP D3V3G2 LINKER SEQADV 6TRP GLY A 54 UNP D3V3G2 LINKER SEQADV 6TRP SER A 55 UNP D3V3G2 LINKER SEQADV 6TRP GLY A 56 UNP D3V3G2 LINKER SEQADV 6TRP SER A 57 UNP D3V3G2 LINKER SEQADV 6TRP GLY A 58 UNP D3V3G2 LINKER SEQADV 6TRP TYR A 59 UNP D3V3G2 LINKER SEQRES 1 A 93 MET ASN ILE ASN GLU GLN THR LEU ASP LYS LEU ARG GLN SEQRES 2 A 93 ALA VAL LEU GLN LYS LYS ILE LYS GLU ARG ILE GLN ASN SEQRES 3 A 93 SER LEU SER THR GLU LYS TYR GLY SER GLY SER GLY SER SEQRES 4 A 93 GLY SER GLY SER GLY SER GLY SER GLY SER GLY SER GLY SEQRES 5 A 93 SER GLY SER GLY SER GLY TYR GLN ILE GLU THR PHE PHE SEQRES 6 A 93 ALA GLN ASP ILE GLU SER VAL GLN LYS GLU LEU GLU ASN SEQRES 7 A 93 LEU SER GLU GLU GLU LEU LEU ALA MET LEU ASN GLY ASP SEQRES 8 A 93 GLN GLN HELIX 1 AA1 THR A 7 SER A 27 1 21 HELIX 2 AA2 PHE A 3293 GLU A 3305 1 13 HELIX 3 AA3 SER A 3308 GLY A 3318 1 11 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