HEADER TRANSFERASE 05-MAR-15 4YL7 TITLE CRYSTAL STRUCTURE OF THE INDOLE PRENYLTRANSFERASE MPND FROM TITLE 2 MARINACTINOSPORA THERMOTOLERANS COMPND MOL_ID: 1; COMPND 2 MOLECULE: AROMATIC PRENYLTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MARINACTINOSPORA THERMOTOLERANS; SOURCE 3 ORGANISM_TAXID: 531310; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BLR; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET22B KEYWDS TRANSFERASE, PT-FOLD, INDOLACTAM V, INDOLE PRENYLTRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR T.MORI,H.MORITA,I.ABE REVDAT 4 08-NOV-23 4YL7 1 REMARK REVDAT 3 05-FEB-20 4YL7 1 REMARK REVDAT 2 20-APR-16 4YL7 1 JRNL REVDAT 1 16-MAR-16 4YL7 0 JRNL AUTH T.MORI,L.ZHANG,T.AWAKAWA,S.HOSHINO,M.OKADA,H.MORITA,I.ABE JRNL TITL MANIPULATION OF PRENYLATION REACTIONS BY STRUCTURE-BASED JRNL TITL 2 ENGINEERING OF BACTERIAL INDOLACTAM PRENYLTRANSFERASES. JRNL REF NAT COMMUN V. 7 10849 2016 JRNL REFN ESSN 2041-1723 JRNL PMID 26952246 JRNL DOI 10.1038/NCOMMS10849 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.2_1309) 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.14 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 44640 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2232 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 34.1467 - 4.0320 0.99 2834 150 0.1835 0.1603 REMARK 3 2 4.0320 - 3.2011 1.00 2727 143 0.1665 0.1861 REMARK 3 3 3.2011 - 2.7967 1.00 2689 142 0.1846 0.2120 REMARK 3 4 2.7967 - 2.5410 1.00 2668 140 0.1929 0.2319 REMARK 3 5 2.5410 - 2.3590 1.00 2671 141 0.1856 0.2105 REMARK 3 6 2.3590 - 2.2199 1.00 2637 138 0.1712 0.2000 REMARK 3 7 2.2199 - 2.1088 1.00 2660 140 0.1727 0.1951 REMARK 3 8 2.1088 - 2.0170 1.00 2649 140 0.1668 0.2163 REMARK 3 9 2.0170 - 1.9393 1.00 2634 138 0.1717 0.2070 REMARK 3 10 1.9393 - 1.8724 1.00 2619 138 0.1830 0.2153 REMARK 3 11 1.8724 - 1.8139 1.00 2639 139 0.1812 0.2668 REMARK 3 12 1.8139 - 1.7620 1.00 2639 139 0.1929 0.2218 REMARK 3 13 1.7620 - 1.7156 1.00 2624 138 0.1819 0.2281 REMARK 3 14 1.7156 - 1.6738 1.00 2580 136 0.1871 0.2303 REMARK 3 15 1.6738 - 1.6357 1.00 2630 139 0.1972 0.2397 REMARK 3 16 1.6357 - 1.6009 0.96 2508 131 0.2162 0.2937 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.130 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 : 0.006 2871 REMARK 3 ANGLE : 1.127 3923 REMARK 3 CHIRALITY : 0.074 414 REMARK 3 PLANARITY : 0.006 530 REMARK 3 DIHEDRAL : 12.129 1032 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 4YL7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-MAR-15. REMARK 100 THE DEPOSITION ID IS D_1000207601. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-NOV-13 REMARK 200 TEMPERATURE (KELVIN) : 173 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS XDS-OSX10.9.4_DARWIN13.3.0 REMARK 200 DATA SCALING SOFTWARE : XSCALE XDS REMARK 200 -OSX10.9.4_DARWIN13.3.0 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44641 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 7.180 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 25.0400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.3 REMARK 200 DATA REDUNDANCY IN SHELL : 6.95 REMARK 200 R MERGE FOR SHELL (I) : 0.31500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.830 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP CCP4-6.4.0 REMARK 200 STARTING MODEL: 4YZJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM TRIS-HCL (PH8.5), 1470 MM REMARK 280 (NH4)2SO4, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 23.33000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 66.34000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.85000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 66.34000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.33000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.85000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 MET A 1 REMARK 465 ASP A 340 REMARK 465 GLY A 341 REMARK 465 GLU A 342 REMARK 465 GLY A 343 REMARK 465 GLU A 376 REMARK 465 HIS A 377 REMARK 465 HIS A 378 REMARK 465 HIS A 379 REMARK 465 HIS A 380 REMARK 465 HIS A 381 REMARK 465 HIS A 382 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 ARG A 24 -76.50 -111.73 REMARK 500 ASN A 69 40.70 -87.13 REMARK 500 ASP A 228 52.76 -98.86 REMARK 500 HIS A 240 65.11 -104.42 REMARK 500 ILE A 270 -65.02 -102.08 REMARK 500 ASN A 349 -64.76 -95.74 REMARK 500 REMARK 500 REMARK: NULL DBREF 4YL7 A 1 374 UNP I7EIW6 I7EIW6_9ACTO 1 374 SEQADV 4YL7 LEU A 375 UNP I7EIW6 EXPRESSION TAG SEQADV 4YL7 GLU A 376 UNP I7EIW6 EXPRESSION TAG SEQADV 4YL7 HIS A 377 UNP I7EIW6 EXPRESSION TAG SEQADV 4YL7 HIS A 378 UNP I7EIW6 EXPRESSION TAG SEQADV 4YL7 HIS A 379 UNP I7EIW6 EXPRESSION TAG SEQADV 4YL7 HIS A 380 UNP I7EIW6 EXPRESSION TAG SEQADV 4YL7 HIS A 381 UNP I7EIW6 EXPRESSION TAG SEQADV 4YL7 HIS A 382 UNP I7EIW6 EXPRESSION TAG SEQRES 1 A 382 MET ALA GLY ASP PRO PHE VAL ASP ASN GLY THR VAL SER SEQRES 2 A 382 SER GLN ARG PRO LEU ARG ALA VAL PRO GLY ARG TYR PRO SEQRES 3 A 382 PRO GLY ALA THR HIS LEU ASP ALA ALA VAL ASP THR LEU SEQRES 4 A 382 VAL ARG CYS HIS ALA ALA LEU GLY ARG ALA PRO SER GLU SEQRES 5 A 382 ALA GLU ALA ALA VAL CYS LEU LEU ARG ARG LEU TRP GLY SEQRES 6 A 382 ARG TRP GLY ASN THR PRO VAL GLU ARG PRO GLY TRP ARG SEQRES 7 A 382 SER TYR VAL ALA VAL ASP GLY SER PRO PHE GLU LEU SER SEQRES 8 A 382 ALA ALA TRP ASN GLY ASP GLY PRO ALA GLU VAL ARG VAL SEQRES 9 A 382 THR VAL GLU ALA THR ALA ASP PRO PRO THR PRO GLU GLY SEQRES 10 A 382 ASN GLN GLU ALA GLY TRP GLU TYR LEU ARG GLY LEU SER SEQRES 11 A 382 ARG HIS PRO GLY ALA ALA THR ALA ARG VAL LEU ALA LEU SEQRES 12 A 382 GLU ASP LEU PHE ARG PRO GLN THR PRO HIS ASP ARG CYS SEQRES 13 A 382 TRP ILE MET HIS GLY MET ALA SER ARG PRO GLY ALA ASP SEQRES 14 A 382 PRO LEU PHE LYS VAL TYR LEU ASP PRO ASP ALA ARG GLY SEQRES 15 A 382 ALA ALA GLU ALA PRO SER VAL LEU ASP GLU ALA MET ASP SEQRES 16 A 382 ARG LEU GLY VAL ARG ALA ALA TRP GLN GLY LEU ARG GLY SEQRES 17 A 382 TRP LEU ASP GLU HIS GLY GLY SER GLY ARG ILE GLY SER SEQRES 18 A 382 LEU ALA LEU ASP LEU ALA ASP THR ASP ASP ALA ARG VAL SEQRES 19 A 382 LYS VAL TYR VAL GLN HIS ALA GLY LEU ASP TRP ALA ASP SEQRES 20 A 382 ILE ASP ARG GLN ALA ALA VAL ALA ARG GLY HIS VAL PRO SEQRES 21 A 382 GLY ALA PHE SER ALA ALA LEU GLU GLU ILE THR GLY THR SEQRES 22 A 382 GLU VAL PRO PRO HIS LYS PRO PRO VAL THR CYS PHE ALA SEQRES 23 A 382 PHE HIS ARG GLY VAL GLY VAL PRO THR ALA ALA THR LEU SEQRES 24 A 382 TYR ILE PRO MET PRO ALA GLY VAL PRO GLU SER ASP ALA SEQRES 25 A 382 ARG ARG ARG SER ALA ALA PHE MET ARG ARG SER GLY LEU SEQRES 26 A 382 ASP SER ALA ALA TYR LEU ALA PHE LEU ALA ALA ALA THR SEQRES 27 A 382 GLY ASP GLY GLU GLY VAL ARG ALA LEU GLN ASN PHE VAL SEQRES 28 A 382 ALA TYR ARG PRO ALA ALA PRO GLY GLY ARG PRO ARG PHE SEQRES 29 A 382 ALA CYS TYR VAL ALA PRO GLY LEU TYR ARG LEU GLU HIS SEQRES 30 A 382 HIS HIS HIS HIS HIS FORMUL 2 HOH *363(H2 O) HELIX 1 AA1 THR A 30 LEU A 46 1 17 HELIX 2 AA2 ALA A 49 ASN A 69 1 21 HELIX 3 AA3 THR A 114 SER A 130 1 17 HELIX 4 AA4 THR A 137 ALA A 142 1 6 HELIX 5 AA5 LEU A 143 ARG A 148 1 6 HELIX 6 AA6 GLY A 182 ALA A 184 5 3 HELIX 7 AA7 GLU A 185 LEU A 197 1 13 HELIX 8 AA8 VAL A 199 GLU A 212 1 14 HELIX 9 AA9 ASP A 244 ALA A 252 1 9 HELIX 10 AB1 ALA A 253 ALA A 255 5 3 HELIX 11 AB2 GLY A 261 THR A 271 1 11 HELIX 12 AB3 PRO A 308 SER A 323 1 16 HELIX 13 AB4 ASP A 326 GLY A 339 1 14 SHEET 1 AA1 2 GLY A 10 THR A 11 0 SHEET 2 AA1 2 TRP A 77 ARG A 78 -1 O ARG A 78 N GLY A 10 SHEET 1 AA211 PHE A 88 ASN A 95 0 SHEET 2 AA211 GLU A 101 VAL A 106 -1 O ARG A 103 N SER A 91 SHEET 3 AA211 ILE A 158 SER A 164 -1 O SER A 164 N VAL A 102 SHEET 4 AA211 LEU A 171 LEU A 176 -1 O LEU A 171 N ALA A 163 SHEET 5 AA211 ILE A 219 ASP A 225 -1 O LEU A 222 N LEU A 176 SHEET 6 AA211 VAL A 234 GLN A 239 -1 O LYS A 235 N ALA A 223 SHEET 7 AA211 VAL A 282 PHE A 287 -1 O THR A 283 N VAL A 238 SHEET 8 AA211 ALA A 296 ILE A 301 -1 O TYR A 300 N VAL A 282 SHEET 9 AA211 GLN A 348 ARG A 354 -1 O TYR A 353 N LEU A 299 SHEET 10 AA211 ARG A 363 VAL A 368 -1 O ARG A 363 N ARG A 354 SHEET 11 AA211 PHE A 88 ASN A 95 -1 N TRP A 94 O PHE A 364 CISPEP 1 ASP A 111 PRO A 112 0 0.54 CRYST1 46.660 53.700 132.680 90.00 90.00 90.00 P 21 21 21 4 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 0.021432 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018622 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007537 0.00000