HEADER BIOSYNTHETIC PROTEIN 20-MAR-23 8IS2 TITLE CRYSTAL STRUCTURE OF A POLYKETIDE AROMATASE/CYCLASE ABX(+)D FROM TITLE 2 ACTINOMYCETES SP. MA7150. COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYCLASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: POLYKETIDE AROMATASE/CYCLASE ABX(+)D; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: THE SEQUENCE REFERENCE FOR ACTINOMYCETES SP. MA7150 IS COMPND 7 NOT AVAILABLE AT THE TIME OF BIOCURATION. CURRENT REFERENCE IS COMPND 8 A0A2U3TEK9. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: UNCULTURED ACTINOMYCETE; SOURCE 3 ORGANISM_TAXID: 100235; SOURCE 4 GENE: ABXD; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS AROMATASE, CYCLASE, POLYKETIDE, BIOSYNTHETIC PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.LUO,X.CHEN REVDAT 2 20-MAR-24 8IS2 1 JRNL REVDAT 1 28-FEB-24 8IS2 0 JRNL AUTH K.JIANG,X.CHEN,X.YAN,G.LI,Z.LIN,Z.DENG,S.LUO,X.QU JRNL TITL AN UNUSUAL AROMATASE/CYCLASE PROGRAMS THE FORMATION OF THE JRNL TITL 2 PHENYLDIMETHYLANTHRONE FRAMEWORK IN ANTHRABENZOXOCINONES AND JRNL TITL 3 FASAMYCIN. JRNL REF PROC.NATL.ACAD.SCI.USA V. 121 22121 2024 JRNL REFN ESSN 1091-6490 JRNL PMID 38446858 JRNL DOI 10.1073/PNAS.2321722121 REMARK 2 REMARK 2 RESOLUTION. 1.32 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.32 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.05 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.970 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : 49536 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.227 REMARK 3 R VALUE (WORKING SET) : 0.224 REMARK 3 FREE R VALUE : 0.275 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.850 REMARK 3 FREE R VALUE TEST SET COUNT : 2404 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 21.0500 - 3.4000 0.95 2670 142 0.1908 0.2648 REMARK 3 2 3.3900 - 2.7000 0.97 2777 122 0.2136 0.2531 REMARK 3 3 2.7000 - 2.3600 0.96 2749 141 0.2421 0.2730 REMARK 3 4 2.3600 - 2.1400 0.95 2664 136 0.2344 0.3047 REMARK 3 5 2.1400 - 1.9900 0.96 2755 162 0.2354 0.2686 REMARK 3 6 1.9900 - 1.8700 0.97 2710 153 0.2578 0.2650 REMARK 3 7 1.8700 - 1.7800 0.98 2773 153 0.2641 0.2815 REMARK 3 8 1.7800 - 1.7000 0.98 2778 124 0.2212 0.3223 REMARK 3 9 1.7000 - 1.6300 0.98 2814 151 0.2527 0.3186 REMARK 3 10 1.6300 - 1.5800 0.98 2810 120 0.2631 0.3193 REMARK 3 11 1.5800 - 1.5300 0.98 2763 155 0.2349 0.2679 REMARK 3 12 1.5300 - 1.4800 0.98 2784 141 0.2364 0.3222 REMARK 3 13 1.4800 - 1.4500 0.98 2792 164 0.2604 0.2881 REMARK 3 14 1.4500 - 1.4100 0.99 2831 113 0.2595 0.3154 REMARK 3 15 1.4100 - 1.3800 0.99 2767 132 0.2617 0.2974 REMARK 3 16 1.3800 - 1.3500 0.99 2872 126 0.2749 0.3181 REMARK 3 17 1.3500 - 1.3200 0.99 2823 169 0.2938 0.3104 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 35.800 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.005 1716 REMARK 3 ANGLE : 0.754 2322 REMARK 3 CHIRALITY : 0.075 253 REMARK 3 PLANARITY : 0.007 300 REMARK 3 DIHEDRAL : 14.009 639 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 8IS2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 29-MAR-23. REMARK 100 THE DEPOSITION ID IS D_1300036259. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-DEC-20 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 8.1 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979191 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49575 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.320 REMARK 200 RESOLUTION RANGE LOW (A) : 38.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 200 DATA REDUNDANCY : 2.600 REMARK 200 R MERGE (I) : 0.02600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.32 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.39 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.38000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MORDA REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.25 M HEPES, 60% TACSIMATE, 0.17 M REMARK 280 NDSB-211, PH 8.1, LIQUID DIFFUSION, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 24.91667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 49.83333 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4220 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11960 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 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 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 GLY A -3 REMARK 465 PRO A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 GLY A 88 REMARK 465 ALA A 89 REMARK 465 TRP A 90 REMARK 465 GLY A 91 REMARK 465 SER A 92 REMARK 465 VAL A 93 REMARK 465 GLU A 94 REMARK 465 GLN A 112 REMARK 465 PRO A 113 REMARK 465 GLY B -3 REMARK 465 PRO B -2 REMARK 465 SER B -1 REMARK 465 HIS B 0 REMARK 465 MET B 1 REMARK 465 ASP B 56 REMARK 465 GLU B 57 REMARK 465 ALA B 58 REMARK 465 LEU B 59 REMARK 465 SER B 60 REMARK 465 LYS B 61 REMARK 465 THR B 62 REMARK 465 LEU B 63 REMARK 465 THR B 64 REMARK 465 PRO B 65 REMARK 465 GLN B 66 REMARK 465 HIS B 67 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 LYS A 46 -123.49 57.91 REMARK 500 LYS B 46 -120.20 48.86 REMARK 500 SER B 92 -19.10 85.37 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 282 DISTANCE = 5.86 ANGSTROMS REMARK 525 HOH A 283 DISTANCE = 5.95 ANGSTROMS REMARK 525 HOH A 284 DISTANCE = 6.11 ANGSTROMS REMARK 525 HOH B 267 DISTANCE = 6.41 ANGSTROMS REMARK 525 HOH B 268 DISTANCE = 7.82 ANGSTROMS DBREF1 8IS2 A 1 113 UNP A0A2U3TEK9_UNCAC DBREF2 8IS2 A A0A2U3TEK9 1 113 DBREF1 8IS2 B 1 113 UNP A0A2U3TEK9_UNCAC DBREF2 8IS2 B A0A2U3TEK9 1 113 SEQADV 8IS2 GLY A -3 UNP A0A2U3TEK EXPRESSION TAG SEQADV 8IS2 PRO A -2 UNP A0A2U3TEK EXPRESSION TAG SEQADV 8IS2 SER A -1 UNP A0A2U3TEK EXPRESSION TAG SEQADV 8IS2 HIS A 0 UNP A0A2U3TEK EXPRESSION TAG SEQADV 8IS2 GLY B -3 UNP A0A2U3TEK EXPRESSION TAG SEQADV 8IS2 PRO B -2 UNP A0A2U3TEK EXPRESSION TAG SEQADV 8IS2 SER B -1 UNP A0A2U3TEK EXPRESSION TAG SEQADV 8IS2 HIS B 0 UNP A0A2U3TEK EXPRESSION TAG SEQRES 1 A 117 GLY PRO SER HIS MET ALA THR THR LEU ILE VAL ALA ARG SEQRES 2 A 117 LEU LYS PRO GLY ASP HIS ARG ASP GLN ILE SER ARG LEU SEQRES 3 A 117 PHE ALA GLU SER ASP THR THR GLU LEU PRO ASP LEU VAL SEQRES 4 A 117 GLY VAL GLN GLU ARG ARG LEU LEU THR PHE LYS ASP LEU SEQRES 5 A 117 TYR PHE HIS LEU VAL ARG THR ASP GLU ALA LEU SER LYS SEQRES 6 A 117 THR LEU THR PRO GLN HIS ASP HIS PRO LEU PHE ARG SER SEQRES 7 A 117 ILE SER GLU ALA MET ASP GLU TYR VAL THR PRO TYR GLU SEQRES 8 A 117 GLY ALA TRP GLY SER VAL GLU GLN ALA SER ALA ARG GLN SEQRES 9 A 117 PHE TYR HIS TRP LYS ARG GLY LEU GLY ARG VAL GLN PRO SEQRES 1 B 117 GLY PRO SER HIS MET ALA THR THR LEU ILE VAL ALA ARG SEQRES 2 B 117 LEU LYS PRO GLY ASP HIS ARG ASP GLN ILE SER ARG LEU SEQRES 3 B 117 PHE ALA GLU SER ASP THR THR GLU LEU PRO ASP LEU VAL SEQRES 4 B 117 GLY VAL GLN GLU ARG ARG LEU LEU THR PHE LYS ASP LEU SEQRES 5 B 117 TYR PHE HIS LEU VAL ARG THR ASP GLU ALA LEU SER LYS SEQRES 6 B 117 THR LEU THR PRO GLN HIS ASP HIS PRO LEU PHE ARG SER SEQRES 7 B 117 ILE SER GLU ALA MET ASP GLU TYR VAL THR PRO TYR GLU SEQRES 8 B 117 GLY ALA TRP GLY SER VAL GLU GLN ALA SER ALA ARG GLN SEQRES 9 B 117 PHE TYR HIS TRP LYS ARG GLY LEU GLY ARG VAL GLN PRO FORMUL 3 HOH *152(H2 O) HELIX 1 AA1 HIS A 15 ASP A 27 1 13 HELIX 2 AA2 GLU A 30 GLY A 36 1 7 HELIX 3 AA3 GLU A 57 SER A 60 5 4 HELIX 4 AA4 HIS A 69 ASP A 80 1 12 HELIX 5 AA5 HIS B 15 ASP B 27 1 13 HELIX 6 AA6 GLU B 30 GLY B 36 1 7 HELIX 7 AA7 HIS B 69 MET B 79 1 11 SHEET 1 AA1 6 VAL A 83 THR A 84 0 SHEET 2 AA1 6 ALA A 2 LEU A 10 -1 N ARG A 9 O THR A 84 SHEET 3 AA1 6 LEU A 48 THR A 55 -1 O TYR A 49 N ALA A 8 SHEET 4 AA1 6 VAL A 37 PHE A 45 -1 N GLN A 38 O ARG A 54 SHEET 5 AA1 6 ARG B 99 LYS B 105 -1 O ARG B 99 N THR A 44 SHEET 6 AA1 6 GLY B 109 GLN B 112 -1 O GLY B 109 N LYS B 105 SHEET 1 AA2 6 GLY A 109 ARG A 110 0 SHEET 2 AA2 6 ARG A 99 LYS A 105 -1 N LYS A 105 O GLY A 109 SHEET 3 AA2 6 GLU B 39 PHE B 45 -1 O THR B 44 N ARG A 99 SHEET 4 AA2 6 LEU B 48 ARG B 54 -1 O LEU B 52 N ARG B 41 SHEET 5 AA2 6 THR B 3 LEU B 10 -1 N ALA B 8 O TYR B 49 SHEET 6 AA2 6 VAL B 83 THR B 84 -1 O THR B 84 N ARG B 9 CISPEP 1 GLN B 112 PRO B 113 0 -6.88 CRYST1 50.945 50.945 74.750 90.00 90.00 120.00 P 31 6 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 0.019629 0.011333 0.000000 0.00000 SCALE2 0.000000 0.022666 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013378 0.00000