HEADER BIOSYNTHETIC PROTEIN 07-AUG-23 8TQG TITLE CRYSTAL STRUCTURE OF MTB PKS13 THIOESTERASE DOMAIN IN COMPLEX WITH TITLE 2 INHIBITOR X20419 COMPND MOL_ID: 1; COMPND 2 MOLECULE: POLYKETIDE SYNTHASE PKS13; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TERMINATION POLYKETIDE SYNTHASE; COMPND 5 EC: 2.3.1.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 1773; SOURCE 4 GENE: PKS13, RV3800C; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS POLYKETIDE SYNTHASE, THIOESTERASE, BIOSYNTHETIC PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR I.V.KRIEGER,J.C.SACCHETTINI REVDAT 2 22-MAY-24 8TQG 1 JRNL REVDAT 1 24-APR-24 8TQG 0 JRNL AUTH I.V.KRIEGER,S.YALAMANCHILI,P.DICKSON,C.A.ENGELHART, JRNL AUTH 2 M.D.ZIMMERMAN,J.WOOD,E.CLARY,J.NGUYEN,N.THORNTON, JRNL AUTH 3 P.A.CENTRELLA,B.CHAN,J.W.CUOZZO,M.GENGENBACHER,M.A.GUIE, JRNL AUTH 4 J.P.GUILINGER,C.BIENSTOCK,H.HARTL,C.D.HUPP,R.JETSON,T.SATOH, JRNL AUTH 5 J.T.S.YEOMAN,Y.ZHANG,V.DARTOIS,D.SCHNAPPINGER,A.D.KEEFE, JRNL AUTH 6 J.C.SACCHETTINI JRNL TITL INHIBITORS OF THE THIOESTERASE ACTIVITY OF MYCOBACTERIUM JRNL TITL 2 TUBERCULOSIS PKS13 DISCOVERED USING DNA-ENCODED CHEMICAL JRNL TITL 3 LIBRARY SCREENING. JRNL REF ACS INFECT DIS. V. 10 1561 2024 JRNL REFN ESSN 2373-8227 JRNL PMID 38577994 JRNL DOI 10.1021/ACSINFECDIS.3C00592 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 59.29 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 15293 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.246 REMARK 3 R VALUE (WORKING SET) : 0.242 REMARK 3 FREE R VALUE : 0.313 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 796 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 59.2900 - 4.0000 0.99 2582 161 0.1906 0.2612 REMARK 3 2 4.0000 - 3.1700 0.98 2428 125 0.2454 0.3198 REMARK 3 3 3.1700 - 2.7700 0.99 2388 144 0.2831 0.3878 REMARK 3 4 2.7700 - 2.5200 0.97 2378 114 0.3073 0.3959 REMARK 3 5 2.5200 - 2.3400 0.99 2369 130 0.3360 0.4207 REMARK 3 6 2.3400 - 2.2000 0.98 2352 122 0.3916 0.4437 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.391 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 39.364 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 49.04 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 62.93 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.008 2287 REMARK 3 ANGLE : 1.008 3110 REMARK 3 CHIRALITY : 0.060 324 REMARK 3 PLANARITY : 0.012 412 REMARK 3 DIHEDRAL : 9.285 331 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8TQG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-AUG-23. REMARK 100 THE DEPOSITION ID IS D_1000276391. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-SEP-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.03317 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15367 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 66.630 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.11300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.27 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 2.24000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.79 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS-HCL, 2.0-1.8 M AMMONIUM REMARK 280 SULFATE, 2%-5% V/V PPG P400, PH 8.5, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 64.97650 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 33.31300 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 33.31300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 32.48825 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 33.31300 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 33.31300 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 97.46475 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 33.31300 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 33.31300 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 32.48825 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 33.31300 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 33.31300 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 97.46475 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 64.97650 REMARK 290 REMARK 290 REMARK: NULL 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 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 SER A 1448 REMARK 465 ASN A 1449 REMARK 465 ALA A 1450 REMARK 465 SER A 1728 REMARK 465 GLU A 1729 REMARK 465 VAL A 1730 REMARK 465 GLY A 1731 REMARK 465 LYS A 1732 REMARK 465 GLN A 1733 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 PRO A1492 155.74 -43.69 REMARK 500 ALA A1493 -83.85 -55.77 REMARK 500 ASP A1494 43.41 -79.21 REMARK 500 SER A1533 -140.36 62.53 REMARK 500 PHE A1590 34.33 -90.65 REMARK 500 ASN A1591 -133.63 49.18 REMARK 500 VAL A1592 70.42 55.59 REMARK 500 PRO A1595 -155.32 -69.76 REMARK 500 ILE A1695 -5.13 -143.54 REMARK 500 ALA A1718 -43.49 173.99 REMARK 500 ASP A1725 6.14 -59.45 REMARK 500 REMARK 500 REMARK: NULL DBREF 8TQG A 1451 1733 UNP I6X8D2 PKS13_MYCTU 1451 1733 SEQADV 8TQG SER A 1448 UNP I6X8D2 EXPRESSION TAG SEQADV 8TQG ASN A 1449 UNP I6X8D2 EXPRESSION TAG SEQADV 8TQG ALA A 1450 UNP I6X8D2 EXPRESSION TAG SEQRES 1 A 286 SER ASN ALA GLN ILE ASP GLY PHE VAL ARG THR LEU ARG SEQRES 2 A 286 ALA ARG PRO GLU ALA GLY GLY LYS VAL PRO VAL PHE VAL SEQRES 3 A 286 PHE HIS PRO ALA GLY GLY SER THR VAL VAL TYR GLU PRO SEQRES 4 A 286 LEU LEU GLY ARG LEU PRO ALA ASP THR PRO MET TYR GLY SEQRES 5 A 286 PHE GLU ARG VAL GLU GLY SER ILE GLU GLU ARG ALA GLN SEQRES 6 A 286 GLN TYR VAL PRO LYS LEU ILE GLU MET GLN GLY ASP GLY SEQRES 7 A 286 PRO TYR VAL LEU VAL GLY TRP SER LEU GLY GLY VAL LEU SEQRES 8 A 286 ALA TYR ALA CYS ALA ILE GLY LEU ARG ARG LEU GLY LYS SEQRES 9 A 286 ASP VAL ARG PHE VAL GLY LEU ILE ASP ALA VAL ARG ALA SEQRES 10 A 286 GLY GLU GLU ILE PRO GLN THR LYS GLU GLU ILE ARG LYS SEQRES 11 A 286 ARG TRP ASP ARG TYR ALA ALA PHE ALA GLU LYS THR PHE SEQRES 12 A 286 ASN VAL THR ILE PRO ALA ILE PRO TYR GLU GLN LEU GLU SEQRES 13 A 286 GLU LEU ASP ASP GLU GLY GLN VAL ARG PHE VAL LEU ASP SEQRES 14 A 286 ALA VAL SER GLN SER GLY VAL GLN ILE PRO ALA GLY ILE SEQRES 15 A 286 ILE GLU HIS GLN ARG THR SER TYR LEU ASP ASN ARG ALA SEQRES 16 A 286 ILE ASP THR ALA GLN ILE GLN PRO TYR ASP GLY HIS VAL SEQRES 17 A 286 THR LEU TYR MET ALA ASP ARG TYR HIS ASP ASP ALA ILE SEQRES 18 A 286 MET PHE GLU PRO ARG TYR ALA VAL ARG GLN PRO ASP GLY SEQRES 19 A 286 GLY TRP GLY GLU TYR VAL SER ASP LEU GLU VAL VAL PRO SEQRES 20 A 286 ILE GLY GLY GLU HIS ILE GLN ALA ILE ASP GLU PRO ILE SEQRES 21 A 286 ILE ALA LYS VAL GLY GLU HIS MET SER ARG ALA LEU GLY SEQRES 22 A 286 GLN ILE GLU ALA ASP ARG THR SER GLU VAL GLY LYS GLN HET JR0 A1801 46 HET SO4 A1802 5 HET SO4 A1803 5 HETNAM JR0 N-BENZYL-2-{4-[4-(4,5-DIMETHOXY-1H-INDOLE-2-CARBONYL) HETNAM 2 JR0 PIPERAZINE-1-CARBONYL]PIPERIDIN-1-YL}-6- HETNAM 3 JR0 METHYLPYRIMIDINE-4-CARBOXAMIDE HETNAM SO4 SULFATE ION FORMUL 2 JR0 C34 H39 N7 O5 FORMUL 3 SO4 2(O4 S 2-) FORMUL 5 HOH *13(H2 O) HELIX 1 AA1 SER A 1480 VAL A 1483 5 4 HELIX 2 AA2 TYR A 1484 ARG A 1490 1 7 HELIX 3 AA3 SER A 1506 GLY A 1523 1 18 HELIX 4 AA4 SER A 1533 LEU A 1549 1 17 HELIX 5 AA5 THR A 1571 PHE A 1590 1 20 HELIX 6 AA6 GLU A 1600 LEU A 1605 1 6 HELIX 7 AA7 ASP A 1606 GLN A 1620 1 15 HELIX 8 AA8 PRO A 1626 ALA A 1646 1 21 HELIX 9 AA9 HIS A 1664 GLU A 1671 1 8 HELIX 10 AB1 PRO A 1672 VAL A 1676 5 5 HELIX 11 AB2 ILE A 1707 ASP A 1725 1 19 SHEET 1 AA1 8 ILE A1452 ASP A1453 0 SHEET 2 AA1 8 VAL A1456 ARG A1460 -1 O VAL A1456 N ASP A1453 SHEET 3 AA1 8 MET A1497 PHE A1500 -1 O GLY A1499 N ARG A1457 SHEET 4 AA1 8 VAL A1471 PHE A1474 1 N VAL A1473 O PHE A1500 SHEET 5 AA1 8 TYR A1527 TRP A1532 1 O VAL A1530 N PHE A1472 SHEET 6 AA1 8 VAL A1553 ILE A1559 1 O ILE A1559 N GLY A1531 SHEET 7 AA1 8 VAL A1655 MET A1659 1 O TYR A1658 N LEU A1558 SHEET 8 AA1 8 LEU A1690 PRO A1694 1 O GLU A1691 N LEU A1657 CISPEP 1 GLY A 1525 PRO A 1526 0 -5.41 CISPEP 2 GLU A 1705 PRO A 1706 0 0.56 CRYST1 66.626 66.626 129.953 90.00 90.00 90.00 P 41 21 2 8 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 0.015009 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015009 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007695 0.00000