HEADER PROTEIN BINDING 01-DEC-23 8RAJ TITLE NMR STRUCTURE OF PKS DOCKING DOMAINS COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-KETOACYL SYNTHASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: TRIMETHYLAMINE MONOOXYGENASE; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHYLORUBRUM EXTORQUENS AM1; SOURCE 3 ORGANISM_TAXID: 272630; SOURCE 4 GENE: MEXAM1_META2P0008; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PBG102; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: METHYLORUBRUM EXTORQUENS AM1; SOURCE 10 ORGANISM_TAXID: 272630; SOURCE 11 GENE: MEXAM1_META2P0010; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 14 EXPRESSION_SYSTEM_PLASMID: PBG102 KEYWDS DOCKING DOMAIN, POLYKETIDE SYNTHASE, PROTEIN BINDING EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR S.SCAT,K.J.WEISSMAN,B.CHAGOT REVDAT 2 17-JUL-24 8RAJ 1 JRNL REVDAT 1 05-JUN-24 8RAJ 0 JRNL AUTH S.SCAT,K.J.WEISSMAN,B.CHAGOT JRNL TITL INSIGHTS INTO DOCKING IN MEGASYNTHASES FROM THE JRNL TITL 2 INVESTIGATION OF THE TOBLEROL TRANS -AT POLYKETIDE SYNTHASE: JRNL TITL 3 MANY ALPHA-HELICAL MEANS TO AN END. JRNL REF RSC CHEM BIOL V. 5 669 2024 JRNL REFN ESSN 2633-0679 JRNL PMID 38966669 JRNL DOI 10.1039/D4CB00075G 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 8RAJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-DEC-23. REMARK 100 THE DEPOSITION ID IS D_1292135021. 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 TOBC, 2 MM TOBE, 100 MM SODIUM REMARK 210 PHOSPHATE, 90% H2O/10% D2O; 1 MM REMARK 210 [U-100% 13C; U-100% 15N] TOBE, 2 REMARK 210 MM TOBC, 100 MM SODIUM PHOSPHATE, REMARK 210 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-13C HSQC; 2D 1H-15N HSQC; REMARK 210 3D HNCA; 3D HNCO; 3D HNCACB; 3D REMARK 210 HN(CA)CO; 3D CBCA(CO)NH; 3D HCCH- REMARK 210 TOCSY; 3D CCH-TOCSY; 3D C(CO)NH; REMARK 210 3D H(CCO)NH; 3D 1H-13C NOESY; 3D REMARK 210 1H-15N NOESY; 3D 1H-13C NOESY REMARK 210 AROMATIC; 3D HNHA REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA, NMRFAM-SPARKY, CCPNMR REMARK 210 ANALYSIS ASSIGN REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA 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 A2271 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 ARG B 13 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 4 ARG A2271 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 5 ARG A2271 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 5 ARG B 8 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 7 ARG A2271 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 8 ARG A2278 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 9 ARG A2278 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 9 ARG B 13 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 10 ARG A2271 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 10 ARG B 13 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 12 ARG A2241 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 12 ARG A2278 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 13 ARG B 8 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 15 ARG A2271 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 15 ARG A2278 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 16 ARG A2271 NE - CZ - NH2 ANGL. DEV. = 3.0 DEGREES REMARK 500 16 ARG A2278 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 16 ARG B 13 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 17 ARG A2278 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 18 ARG A2271 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 18 ARG B 8 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 18 ARG B 13 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 19 ARG A2271 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 19 ARG A2278 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 TYR B -1 -138.44 53.55 REMARK 500 1 THR B 2 -75.92 -106.94 REMARK 500 1 SER B 11 -104.92 -119.07 REMARK 500 1 THR B 34 -108.28 -124.57 REMARK 500 2 LYS A2234 125.95 81.05 REMARK 500 2 VAL A2237 16.70 -148.49 REMARK 500 2 LEU A2251 -145.94 -92.66 REMARK 500 2 ILE B 32 -115.72 -88.67 REMARK 500 2 SER B 37 140.47 83.42 REMARK 500 2 ASP B 43 30.40 -153.42 REMARK 500 3 SER A2223 -134.89 51.34 REMARK 500 3 ALA A2227 49.20 -150.32 REMARK 500 3 ASN A2229 84.86 179.60 REMARK 500 3 MET B 1 -154.05 60.20 REMARK 500 3 HIS B 3 23.05 93.14 REMARK 500 4 ASP A2238 44.44 -150.00 REMARK 500 4 VAL B 9 99.67 81.56 REMARK 500 4 ALA B 42 -158.72 62.85 REMARK 500 4 ASP B 43 -65.29 -150.03 REMARK 500 5 GLU A2228 -148.35 60.10 REMARK 500 5 PRO A2232 44.06 -91.52 REMARK 500 5 LYS A2245 -137.40 61.18 REMARK 500 5 TYR B -1 40.51 -148.60 REMARK 500 5 PHE B 4 -146.26 -89.81 REMARK 500 5 ARG B 8 45.70 -155.33 REMARK 500 5 ALA B 15 -138.47 59.00 REMARK 500 6 ASP A2248 35.81 -151.30 REMARK 500 6 LEU A2251 -136.15 -107.71 REMARK 500 6 THR B 2 -136.60 42.10 REMARK 500 6 GLU B 5 49.04 -83.04 REMARK 500 7 ALA A2235 45.62 -143.94 REMARK 500 7 PHE B 4 -145.80 63.37 REMARK 500 7 ASP B 6 46.46 -84.60 REMARK 500 8 GLU A2228 11.58 -148.48 REMARK 500 8 ASP A2248 69.51 -117.74 REMARK 500 8 HIS B 3 76.31 -104.35 REMARK 500 8 ASP B 6 54.51 -92.07 REMARK 500 8 ASP B 12 37.92 -88.85 REMARK 500 8 ARG B 13 31.19 -171.32 REMARK 500 8 LEU B 14 -152.20 60.55 REMARK 500 8 ALA B 42 13.32 -149.51 REMARK 500 9 ALA A2227 126.75 85.41 REMARK 500 9 ASP A2233 26.37 -150.09 REMARK 500 9 LYS A2234 -127.39 59.31 REMARK 500 9 SER A2242 116.35 -173.51 REMARK 500 9 HIS B 3 -63.23 -138.29 REMARK 500 10 TYR A2224 -65.12 85.40 REMARK 500 10 ASP A2238 36.35 -150.13 REMARK 500 10 HIS A2240 130.66 -172.30 REMARK 500 10 LYS A2247 16.04 -150.08 REMARK 500 REMARK 500 THIS ENTRY HAS 110 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34886 RELATED DB: BMRB REMARK 900 NMR STRUCTURE OF PKS DOCKING DOMAINS DBREF 8RAJ A 2225 2278 UNP C5B3B7 C5B3B7_METEA 2225 2278 DBREF 8RAJ B 1 44 UNP C5B3B9 C5B3B9_METEA 1 44 SEQADV 8RAJ GLY A 2217 UNP C5B3B7 EXPRESSION TAG SEQADV 8RAJ PRO A 2218 UNP C5B3B7 EXPRESSION TAG SEQADV 8RAJ GLY A 2219 UNP C5B3B7 EXPRESSION TAG SEQADV 8RAJ SER A 2220 UNP C5B3B7 EXPRESSION TAG SEQADV 8RAJ PRO A 2221 UNP C5B3B7 EXPRESSION TAG SEQADV 8RAJ ASN A 2222 UNP C5B3B7 EXPRESSION TAG SEQADV 8RAJ SER A 2223 UNP C5B3B7 EXPRESSION TAG SEQADV 8RAJ TYR A 2224 UNP C5B3B7 EXPRESSION TAG SEQADV 8RAJ GLY B -5 UNP C5B3B9 EXPRESSION TAG SEQADV 8RAJ PRO B -4 UNP C5B3B9 EXPRESSION TAG SEQADV 8RAJ GLY B -3 UNP C5B3B9 EXPRESSION TAG SEQADV 8RAJ SER B -2 UNP C5B3B9 EXPRESSION TAG SEQADV 8RAJ TYR B -1 UNP C5B3B9 EXPRESSION TAG SEQRES 1 A 62 GLY PRO GLY SER PRO ASN SER TYR LEU PRO ALA GLU ASN SEQRES 2 A 62 GLU ASP PRO ASP LYS ALA VAL VAL ASP LEU HIS ARG SER SEQRES 3 A 62 PRO PRO LYS THR LYS ASP PRO ASP LEU THR PRO SER GLY SEQRES 4 A 62 ILE ILE ALA LYS VAL LYS ALA GLY ASP MET THR GLN GLU SEQRES 5 A 62 THR ALA ARG GLU LEU LEU LEU ALA MET ARG SEQRES 1 B 49 GLY PRO GLY SER TYR MET THR HIS PHE GLU ASP HIS ARG SEQRES 2 B 49 VAL GLY SER ASP ARG LEU ALA ALA ASP GLY GLU ILE SER SEQRES 3 B 49 ALA ASP GLU ALA LEU SER MET LEU ASP ALA ILE GLY THR SEQRES 4 B 49 GLY GLN SER THR PRO THR GLY ALA ASP ASP HELIX 1 AA1 THR A 2252 ALA A 2262 1 11 HELIX 2 AA2 THR A 2266 ARG A 2278 1 13 HELIX 3 AA3 SER B 21 ASP B 30 1 10 CISPEP 1 GLY B -5 PRO B -4 2 3.22 CISPEP 2 SER B 37 THR B 38 3 -2.41 CISPEP 3 GLY B 41 ALA B 42 7 4.06 CISPEP 4 PHE B 4 GLU B 5 9 -1.02 CISPEP 5 GLY B -5 PRO B -4 17 -0.88 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