HEADER PROTEIN BINDING 08-NOV-19 6TDN TITLE BAM_5925CDD 5924NDD 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_5925, BAMB_5924; 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 6TDN 1 REMARK REVDAT 2 07-OCT-20 6TDN 1 JRNL REVDAT 1 12-AUG-20 6TDN 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 6TDN 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_1292105308. 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 : 0.1 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; 2D 1H-13C HSQC REMARK 210 AROMATIC; 3D HNCO; 3D CBCA(CO)NH; REMARK 210 3D HNCACB; 3D HCCH-TOCSY; 3D REMARK 210 C(CO)NH; 3D H(CCO)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: 2530 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11820 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 66 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 ARG B 163 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 ARG B 166 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 3 ARG A 33 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 3 ARG A 63 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 3 ARG B 166 NE - CZ - NH2 ANGL. DEV. = 3.9 DEGREES REMARK 500 4 ARG A 63 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 4 ARG B 133 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 5 ARG B 133 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 5 ARG B 163 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 6 ARG A 63 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 6 ARG B 133 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 6 ARG B 166 NE - CZ - NH2 ANGL. DEV. = 3.1 DEGREES REMARK 500 8 ARG A 33 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 8 ARG B 133 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 9 ARG A 33 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 10 ARG A 66 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 10 ARG B 163 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 10 ARG B 163 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 11 ARG A 63 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 14 ARG B 133 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 16 ARG B 163 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 18 ARG B 163 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 19 ARG B 133 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 21 ARG B 163 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 22 ARG A 33 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 22 ARG A 63 NE - CZ - NH2 ANGL. DEV. = 4.5 DEGREES REMARK 500 22 ARG B 163 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 23 ARG B 163 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 24 ARG B 163 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 25 ARG A 63 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 25 ARG B 166 NE - CZ - NH1 ANGL. DEV. = 3.7 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 6 158.39 62.10 REMARK 500 1 ASN A 48 156.85 62.34 REMARK 500 1 ASP A 54 -168.60 56.31 REMARK 500 1 ALA B 106 164.21 62.89 REMARK 500 1 GLU B 134 -176.10 59.38 REMARK 500 1 LYS B 149 142.01 65.46 REMARK 500 1 ASP B 154 -17.46 60.14 REMARK 500 2 ALA A 6 159.02 63.38 REMARK 500 2 SER A 42 169.30 61.93 REMARK 500 2 MET A 47 13.32 58.80 REMARK 500 2 SER A 53 -176.53 60.89 REMARK 500 2 ALA B 106 149.63 65.49 REMARK 500 2 ASN B 148 19.00 58.91 REMARK 500 3 ALA A 6 148.73 62.93 REMARK 500 3 ARG A 33 48.25 -97.37 REMARK 500 3 GLU A 34 171.78 59.62 REMARK 500 3 ALA B 106 165.28 60.48 REMARK 500 4 ALA A 6 161.31 62.05 REMARK 500 4 ALA B 106 160.20 61.92 REMARK 500 4 LEU B 108 -13.29 -142.32 REMARK 500 4 SER B 138 -57.64 -155.89 REMARK 500 4 MET B 147 29.33 47.60 REMARK 500 4 THR B 151 -53.01 -148.02 REMARK 500 4 SER B 152 -40.87 60.34 REMARK 500 4 ASP B 154 -87.28 58.26 REMARK 500 5 SER A 4 140.83 66.32 REMARK 500 5 ALA A 6 156.42 60.94 REMARK 500 5 ASP A 9 54.66 -153.38 REMARK 500 5 ALA B 106 146.18 64.86 REMARK 500 5 LEU B 108 -18.24 -152.74 REMARK 500 5 LYS B 129 -38.84 62.21 REMARK 500 6 ALA A 6 150.24 61.47 REMARK 500 6 TYR B 105 -44.80 63.11 REMARK 500 6 ALA B 106 148.95 62.62 REMARK 500 6 ASP B 154 -38.37 63.42 REMARK 500 7 ALA A 6 150.22 63.11 REMARK 500 7 LEU A 8 -15.77 -140.52 REMARK 500 7 SER A 53 33.73 -74.18 REMARK 500 7 ALA B 106 162.81 62.19 REMARK 500 7 ASP B 109 30.69 -92.93 REMARK 500 7 SER B 152 75.60 -151.46 REMARK 500 7 GLN B 186 -175.33 52.21 REMARK 500 8 ALA A 6 147.58 63.02 REMARK 500 8 ASP A 9 -0.50 -142.68 REMARK 500 8 LEU A 18 -179.91 -69.57 REMARK 500 8 TYR B 105 -42.36 61.81 REMARK 500 8 ALA B 106 147.07 62.61 REMARK 500 8 LEU B 108 -11.56 -152.07 REMARK 500 8 ASP B 109 30.00 -144.36 REMARK 500 8 ASP B 154 -2.48 -144.80 REMARK 500 REMARK 500 THIS ENTRY HAS 137 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 B 166 0.08 SIDE CHAIN REMARK 500 23 ARG B 163 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34448 RELATED DB: BMRB REMARK 900 BAM_5920CDD 5919NDD DOCKING DOMAINS DBREF 6TDN A 6 34 UNP Q0B303 Q0B303_BURCM 2616 2644 DBREF 6TDN A 47 87 UNP Q0B304 Q0B304_BURCM 1 41 DBREF 6TDN B 106 134 UNP Q0B303 Q0B303_BURCM 2616 2644 DBREF 6TDN B 147 187 UNP Q0B304 Q0B304_BURCM 1 41 SEQADV 6TDN GLY A 1 UNP Q0B303 EXPRESSION TAG SEQADV 6TDN PRO A 2 UNP Q0B303 EXPRESSION TAG SEQADV 6TDN GLY A 3 UNP Q0B303 EXPRESSION TAG SEQADV 6TDN SER A 4 UNP Q0B303 EXPRESSION TAG SEQADV 6TDN TYR A 5 UNP Q0B303 EXPRESSION TAG SEQADV 6TDN GLY A 35 UNP Q0B303 LINKER SEQADV 6TDN GLY A 36 UNP Q0B303 LINKER SEQADV 6TDN GLY A 37 UNP Q0B303 LINKER SEQADV 6TDN SER A 38 UNP Q0B303 LINKER SEQADV 6TDN GLY A 39 UNP Q0B303 LINKER SEQADV 6TDN GLY A 40 UNP Q0B303 LINKER SEQADV 6TDN GLY A 41 UNP Q0B303 LINKER SEQADV 6TDN SER A 42 UNP Q0B303 LINKER SEQADV 6TDN GLY A 43 UNP Q0B303 LINKER SEQADV 6TDN GLY A 44 UNP Q0B303 LINKER SEQADV 6TDN GLY A 45 UNP Q0B303 LINKER SEQADV 6TDN SER A 46 UNP Q0B303 LINKER SEQADV 6TDN GLY B 101 UNP Q0B303 EXPRESSION TAG SEQADV 6TDN PRO B 102 UNP Q0B303 EXPRESSION TAG SEQADV 6TDN GLY B 103 UNP Q0B303 EXPRESSION TAG SEQADV 6TDN SER B 104 UNP Q0B303 EXPRESSION TAG SEQADV 6TDN TYR B 105 UNP Q0B303 EXPRESSION TAG SEQADV 6TDN GLY B 135 UNP Q0B303 LINKER SEQADV 6TDN GLY B 136 UNP Q0B303 LINKER SEQADV 6TDN GLY B 137 UNP Q0B303 LINKER SEQADV 6TDN SER B 138 UNP Q0B303 LINKER SEQADV 6TDN GLY B 139 UNP Q0B303 LINKER SEQADV 6TDN GLY B 140 UNP Q0B303 LINKER SEQADV 6TDN GLY B 141 UNP Q0B303 LINKER SEQADV 6TDN SER B 142 UNP Q0B303 LINKER SEQADV 6TDN GLY B 143 UNP Q0B303 LINKER SEQADV 6TDN GLY B 144 UNP Q0B303 LINKER SEQADV 6TDN GLY B 145 UNP Q0B303 LINKER SEQADV 6TDN SER B 146 UNP Q0B303 LINKER SEQRES 1 A 87 GLY PRO GLY SER TYR ALA PRO LEU ASP THR GLU LEU SER SEQRES 2 A 87 GLU ILE GLU GLY LEU GLN ASP ASP ASP LEU ALA ALA LEU SEQRES 3 A 87 LEU GLY LYS GLU PHE ILE ARG GLU GLY GLY GLY SER GLY SEQRES 4 A 87 GLY GLY SER GLY GLY GLY SER MET ASN LYS PRO THR SER SEQRES 5 A 87 SER ASP GLY TRP LYS ASP ASP TYR LEU SER ARG LEU SER SEQRES 6 A 87 ARG LEU SER LYS ASN GLN LEU MET ALA LEU ALA LEU LYS SEQRES 7 A 87 LEU LYS GLN GLN GLN LEU GLU GLN GLY SEQRES 1 B 87 GLY PRO GLY SER TYR ALA PRO LEU ASP THR GLU LEU SER SEQRES 2 B 87 GLU ILE GLU GLY LEU GLN ASP ASP ASP LEU ALA ALA LEU SEQRES 3 B 87 LEU GLY LYS GLU PHE ILE ARG GLU GLY GLY GLY SER GLY SEQRES 4 B 87 GLY GLY SER GLY GLY GLY SER MET ASN LYS PRO THR SER SEQRES 5 B 87 SER ASP GLY TRP LYS ASP ASP TYR LEU SER ARG LEU SER SEQRES 6 B 87 ARG LEU SER LYS ASN GLN LEU MET ALA LEU ALA LEU LYS SEQRES 7 B 87 LEU LYS GLN GLN GLN LEU GLU GLN GLY HELIX 1 AA1 THR A 10 GLU A 16 1 7 HELIX 2 AA2 GLN A 19 GLY A 28 1 10 HELIX 3 AA3 LYS A 29 PHE A 31 5 3 HELIX 4 AA4 GLY A 55 LEU A 67 1 13 HELIX 5 AA5 SER A 68 LEU A 84 1 17 HELIX 6 AA6 ASP B 109 LEU B 118 1 10 HELIX 7 AA7 GLN B 119 GLY B 128 1 10 HELIX 8 AA8 LYS B 129 PHE B 131 5 3 HELIX 9 AA9 GLY B 155 LEU B 167 1 13 HELIX 10 AB1 SER B 168 LEU B 184 1 17 CISPEP 1 GLY A 41 SER A 42 6 0.81 CISPEP 2 MET A 47 ASN A 48 9 6.21 CISPEP 3 SER A 52 SER A 53 10 -1.15 CISPEP 4 SER B 152 SER B 153 12 1.28 CISPEP 5 LYS B 129 GLU B 130 16 1.50 CISPEP 6 GLY B 136 GLY B 137 17 2.17 CISPEP 7 SER B 142 GLY B 143 17 -7.94 CISPEP 8 GLY A 43 GLY A 44 24 -0.01 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