HEADER PROTEIN BINDING 08-NOV-19 6TDM TITLE BAM_5920CDD 5919NDD DOCKING DOMAINS COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-KETOACYL SYNTHASE,BETA-KETOACYL SYNTHASE; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BURKHOLDERIA AMBIFARIA AMMD; SOURCE 3 ORGANISM_TAXID: 339670; SOURCE 4 GENE: BAMB_5920, BAMB_5919; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PBG102 KEYWDS DOCKING DOMAIN, POLYKETIDE SYNTHASE, PROTEIN BINDING EXPDTA SOLUTION NMR NUMMDL 25 AUTHOR F.RISSER,B.CHAGOT REVDAT 3 14-JUN-23 6TDM 1 REMARK REVDAT 2 07-OCT-20 6TDM 1 JRNL REVDAT 1 12-AUG-20 6TDM 0 JRNL AUTH F.RISSER,S.COLLIN,R.DOS SANTOS-MORAIS,A.GRUEZ,B.CHAGOT, JRNL AUTH 2 K.J.WEISSMAN JRNL TITL TOWARDS IMPROVED UNDERSTANDING OF INTERSUBUNIT INTERACTIONS JRNL TITL 2 IN MODULAR POLYKETIDE BIOSYNTHESIS: DOCKING IN THE JRNL TITL 3 ENACYLOXIN IIA POLYKETIDE SYNTHASE. JRNL REF J.STRUCT.BIOL. V. 212 07581 2020 JRNL REFN ESSN 1095-8657 JRNL PMID 32717326 JRNL DOI 10.1016/J.JSB.2020.107581 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6TDM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-NOV-19. REMARK 100 THE DEPOSITION ID IS D_1292105307. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1 MM [U-100% 13C; U-100% 15N] REMARK 210 PROTEIN, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 3D HNCO; 3D CBCA(CO) REMARK 210 NH; 3D HNCACB; 3D HCCH-TOCSY; 3D REMARK 210 H(CCO)NH; 3D C(CO)NH; 3D 1H-15N REMARK 210 NOESY; 3D 1H-13C NOESY ALIPHATIC; REMARK 210 3D 1H-13C NOESY AROMATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA, SPARKY, TOPSPIN REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 25 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2780 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8860 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 19 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 ARG B 119 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 4 ARG A 62 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 6 ARG B 119 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 6 ARG B 150 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 7 ARG B 162 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 8 ARG A 50 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 8 ARG B 162 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 9 ARG B 119 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 10 ARG A 19 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 10 ARG A 50 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 10 ARG B 150 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 10 ARG B 162 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 11 ARG A 19 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 11 ARG A 50 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 11 ARG A 62 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 11 ARG A 63 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 11 ARG B 119 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 11 ARG B 162 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 12 ARG A 63 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 13 ARG B 150 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 14 ARG A 19 NE - CZ - NH2 ANGL. DEV. = 3.0 DEGREES REMARK 500 14 ARG A 50 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 14 ARG B 119 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 15 ARG B 119 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 16 ARG A 19 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 17 ARG B 119 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 17 ARG B 162 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 17 ARG B 163 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 18 ARG A 50 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 18 ARG B 162 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 19 ARG B 162 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 20 ARG A 50 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 20 ARG B 150 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 21 ARG B 150 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 23 ARG A 19 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 23 ARG B 150 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 25 ARG A 62 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 25 ARG B 150 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 25 ARG B 162 NE - CZ - NH1 ANGL. DEV. = 3.3 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 ASP A 6 32.27 -83.48 REMARK 500 1 ASP A 25 45.86 -90.80 REMARK 500 2 ALA A 8 12.73 57.53 REMARK 500 2 ALA B 108 14.17 56.78 REMARK 500 3 ASP A 6 30.61 -77.83 REMARK 500 4 ALA A 7 144.54 64.68 REMARK 500 4 ALA B 108 19.32 54.07 REMARK 500 4 ARG B 162 42.08 -89.53 REMARK 500 5 TYR B 105 108.80 -56.11 REMARK 500 6 ALA A 8 14.78 54.37 REMARK 500 6 ARG A 62 57.79 -95.18 REMARK 500 7 ALA A 8 16.17 57.59 REMARK 500 8 SER A 4 153.16 65.24 REMARK 500 8 ALA A 7 59.87 -140.39 REMARK 500 8 ARG A 62 46.73 -86.25 REMARK 500 8 ASP B 106 42.27 -81.53 REMARK 500 9 SER A 29 -150.48 58.87 REMARK 500 10 ALA A 7 17.40 52.53 REMARK 500 11 ASP A 6 30.27 -79.43 REMARK 500 11 ALA B 107 -33.61 59.83 REMARK 500 12 ASP A 6 39.17 -94.06 REMARK 500 13 ASP A 6 36.69 -76.82 REMARK 500 13 SER B 104 -45.05 -144.64 REMARK 500 13 TYR B 105 -177.76 58.74 REMARK 500 13 SER B 129 -168.90 57.12 REMARK 500 14 TYR A 5 46.77 -80.18 REMARK 500 14 ASP B 106 48.75 -79.58 REMARK 500 15 SER A 4 44.54 -75.48 REMARK 500 15 TYR A 5 172.48 62.98 REMARK 500 15 ALA A 7 131.80 67.48 REMARK 500 15 TYR B 105 171.79 61.38 REMARK 500 15 ALA B 108 24.97 -140.67 REMARK 500 16 TYR A 5 171.29 63.50 REMARK 500 17 ASP B 106 40.17 -80.94 REMARK 500 19 TYR A 5 175.95 59.00 REMARK 500 19 ALA A 8 16.28 57.19 REMARK 500 19 SER B 104 14.36 -144.90 REMARK 500 19 ASP B 106 39.56 -73.60 REMARK 500 20 ALA A 7 83.17 -150.93 REMARK 500 20 ALA B 107 -18.87 64.47 REMARK 500 21 TYR B 105 173.15 57.57 REMARK 500 21 ARG B 162 39.12 -88.77 REMARK 500 23 ASP B 125 47.07 -76.18 REMARK 500 24 ASP A 6 43.14 -78.92 REMARK 500 24 ARG A 63 41.27 -75.43 REMARK 500 24 TYR B 105 12.04 57.17 REMARK 500 24 ALA B 107 -18.51 -142.11 REMARK 500 24 SER B 129 84.35 53.72 REMARK 500 25 ALA A 7 37.26 -150.04 REMARK 500 25 ARG B 163 20.81 -140.15 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 13 ARG A 19 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34447 RELATED DB: BMRB REMARK 900 BAM_5920CDD 5919NDD DOCKING DOMAINS DBREF 6TDM A 6 25 UNP Q0B308 Q0B308_BURCM 2956 2975 DBREF 6TDM A 34 64 UNP Q0B309 Q0B309_BURCM 1 31 DBREF 6TDM B 106 125 UNP Q0B308 Q0B308_BURCM 2956 2975 DBREF 6TDM B 134 164 UNP Q0B309 Q0B309_BURCM 1 31 SEQADV 6TDM GLY A 1 UNP Q0B308 EXPRESSION TAG SEQADV 6TDM PRO A 2 UNP Q0B308 EXPRESSION TAG SEQADV 6TDM GLY A 3 UNP Q0B308 EXPRESSION TAG SEQADV 6TDM SER A 4 UNP Q0B308 EXPRESSION TAG SEQADV 6TDM TYR A 5 UNP Q0B308 EXPRESSION TAG SEQADV 6TDM GLY A 26 UNP Q0B308 LINKER SEQADV 6TDM GLY A 27 UNP Q0B308 LINKER SEQADV 6TDM GLY A 28 UNP Q0B308 LINKER SEQADV 6TDM SER A 29 UNP Q0B308 LINKER SEQADV 6TDM GLY A 30 UNP Q0B308 LINKER SEQADV 6TDM GLY A 31 UNP Q0B308 LINKER SEQADV 6TDM GLY A 32 UNP Q0B308 LINKER SEQADV 6TDM SER A 33 UNP Q0B308 LINKER SEQADV 6TDM GLY B 101 UNP Q0B308 EXPRESSION TAG SEQADV 6TDM PRO B 102 UNP Q0B308 EXPRESSION TAG SEQADV 6TDM GLY B 103 UNP Q0B308 EXPRESSION TAG SEQADV 6TDM SER B 104 UNP Q0B308 EXPRESSION TAG SEQADV 6TDM TYR B 105 UNP Q0B308 EXPRESSION TAG SEQADV 6TDM GLY B 126 UNP Q0B308 LINKER SEQADV 6TDM GLY B 127 UNP Q0B308 LINKER SEQADV 6TDM GLY B 128 UNP Q0B308 LINKER SEQADV 6TDM SER B 129 UNP Q0B308 LINKER SEQADV 6TDM GLY B 130 UNP Q0B308 LINKER SEQADV 6TDM GLY B 131 UNP Q0B308 LINKER SEQADV 6TDM GLY B 132 UNP Q0B308 LINKER SEQADV 6TDM SER B 133 UNP Q0B308 LINKER SEQRES 1 A 64 GLY PRO GLY SER TYR ASP ALA ALA LEU PRO ILE ASP GLU SEQRES 2 A 64 LEU SER ALA LEU LEU ARG GLN GLU MET GLY ASP ASP GLY SEQRES 3 A 64 GLY GLY SER GLY GLY GLY SER MET GLN ASP ILE GLN GLN SEQRES 4 A 64 LEU LEU ALA LYS SER LEU THR GLU ILE LYS ARG LEU LYS SEQRES 5 A 64 ALA ALA ASN GLN ALA LEU GLU GLN ALA ARG ARG GLU SEQRES 1 B 64 GLY PRO GLY SER TYR ASP ALA ALA LEU PRO ILE ASP GLU SEQRES 2 B 64 LEU SER ALA LEU LEU ARG GLN GLU MET GLY ASP ASP GLY SEQRES 3 B 64 GLY GLY SER GLY GLY GLY SER MET GLN ASP ILE GLN GLN SEQRES 4 B 64 LEU LEU ALA LYS SER LEU THR GLU ILE LYS ARG LEU LYS SEQRES 5 B 64 ALA ALA ASN GLN ALA LEU GLU GLN ALA ARG ARG GLU HELIX 1 AA1 PRO A 10 MET A 22 1 13 HELIX 2 AA2 SER A 33 ARG A 62 1 30 HELIX 3 AA3 PRO B 110 MET B 122 1 13 HELIX 4 AA4 SER B 133 ARG B 163 1 31 CISPEP 1 GLY A 31 GLY A 32 2 -3.97 CISPEP 2 GLY A 28 SER A 29 5 -0.22 CISPEP 3 GLY B 131 GLY B 132 5 -1.86 CISPEP 4 SER B 129 GLY B 130 14 -3.94 CISPEP 5 SER A 4 TYR A 5 16 4.97 CISPEP 6 GLY B 128 SER B 129 18 9.75 CISPEP 7 SER B 129 GLY B 130 21 -2.48 CISPEP 8 GLY A 3 SER A 4 22 -4.41 CISPEP 9 GLY A 31 GLY A 32 25 -3.42 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