HEADER HYDROLASE 07-JUN-17 5O70 TITLE STRUCTURE OF THE INACTIVE T.MARITIMA PDE (TM1595) D80N D154N MUTANT TITLE 2 WITH REACTION PRODUCTS 2 AMP COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHODIESTERASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOTOGA MARITIMA (STRAIN ATCC 43589 / MSB8 / SOURCE 3 DSM 3109 / JCM 10099); SOURCE 4 ORGANISM_TAXID: 243274; SOURCE 5 GENE: TM_1595; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PHOSPHODIESTERASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR G.WITTE,D.DREXLER REVDAT 5 17-JAN-24 5O70 1 REMARK REVDAT 4 13-DEC-17 5O70 1 JRNL REVDAT 3 06-DEC-17 5O70 1 REMARK REVDAT 2 15-NOV-17 5O70 1 JRNL REVDAT 1 25-OCT-17 5O70 0 JRNL AUTH D.J.DREXLER,M.MULLER,C.A.ROJAS-CORDOVA,A.M.BANDERA,G.WITTE JRNL TITL STRUCTURAL AND BIOPHYSICAL ANALYSIS OF THE SOLUBLE JRNL TITL 2 DHH/DHHA1-TYPE PHOSPHODIESTERASE TM1595 FROM THERMOTOGA JRNL TITL 3 MARITIMA. JRNL REF STRUCTURE V. 25 1887 2017 JRNL REFN ISSN 1878-4186 JRNL PMID 29107484 JRNL DOI 10.1016/J.STR.2017.10.001 REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12_2829: ???) 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) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.22 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.260 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 106661 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.870 REMARK 3 FREE R VALUE TEST SET COUNT : 5191 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 41.2291 - 4.8136 1.00 3364 200 0.1516 0.1806 REMARK 3 2 4.8136 - 3.8216 1.00 3385 186 0.1114 0.1161 REMARK 3 3 3.8216 - 3.3387 1.00 3391 178 0.1342 0.1870 REMARK 3 4 3.3387 - 3.0336 1.00 3425 179 0.1617 0.1787 REMARK 3 5 3.0336 - 2.8162 1.00 3343 169 0.1697 0.1935 REMARK 3 6 2.8162 - 2.6502 1.00 3426 159 0.1767 0.2088 REMARK 3 7 2.6502 - 2.5175 1.00 3390 175 0.1810 0.2307 REMARK 3 8 2.5175 - 2.4079 1.00 3376 194 0.1731 0.2184 REMARK 3 9 2.4079 - 2.3152 1.00 3388 177 0.1673 0.1766 REMARK 3 10 2.3152 - 2.2353 1.00 3413 141 0.1705 0.2191 REMARK 3 11 2.2353 - 2.1655 1.00 3381 173 0.1608 0.1675 REMARK 3 12 2.1655 - 2.1036 1.00 3386 185 0.1614 0.1832 REMARK 3 13 2.1036 - 2.0482 1.00 3416 185 0.1651 0.2245 REMARK 3 14 2.0482 - 1.9982 1.00 3374 164 0.1742 0.2288 REMARK 3 15 1.9982 - 1.9528 1.00 3375 149 0.1789 0.2117 REMARK 3 16 1.9528 - 1.9112 0.99 3395 200 0.1829 0.2262 REMARK 3 17 1.9112 - 1.8730 0.99 3357 181 0.2012 0.2072 REMARK 3 18 1.8730 - 1.8377 0.99 3351 194 0.2048 0.2358 REMARK 3 19 1.8377 - 1.8048 1.00 3419 180 0.2174 0.2632 REMARK 3 20 1.8048 - 1.7742 0.99 3364 174 0.2199 0.2568 REMARK 3 21 1.7742 - 1.7456 1.00 3369 165 0.2427 0.2267 REMARK 3 22 1.7456 - 1.7188 0.99 3385 170 0.2526 0.2857 REMARK 3 23 1.7188 - 1.6935 1.00 3414 176 0.2649 0.2803 REMARK 3 24 1.6935 - 1.6696 0.99 3351 177 0.2820 0.3564 REMARK 3 25 1.6696 - 1.6471 0.99 3398 134 0.2981 0.3443 REMARK 3 26 1.6471 - 1.6257 0.99 3388 156 0.3088 0.3196 REMARK 3 27 1.6257 - 1.6054 0.99 3346 182 0.3142 0.3694 REMARK 3 28 1.6054 - 1.5860 1.00 3379 181 0.3188 0.3617 REMARK 3 29 1.5860 - 1.5676 0.99 3346 152 0.3308 0.3357 REMARK 3 30 1.5676 - 1.5500 0.97 3375 155 0.3704 0.3504 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.950 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 2810 REMARK 3 ANGLE : 0.849 3834 REMARK 3 CHIRALITY : 0.055 415 REMARK 3 PLANARITY : 0.005 486 REMARK 3 DIHEDRAL : 7.169 2253 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 7 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID -2 THROUGH 39 ) REMARK 3 ORIGIN FOR THE GROUP (A): -12.6915 -22.8578 -9.1350 REMARK 3 T TENSOR REMARK 3 T11: 0.2116 T22: 0.2403 REMARK 3 T33: 0.2322 T12: -0.0723 REMARK 3 T13: -0.0132 T23: 0.0005 REMARK 3 L TENSOR REMARK 3 L11: 2.5080 L22: 5.3314 REMARK 3 L33: 3.8136 L12: 0.2746 REMARK 3 L13: -0.7012 L23: -1.2319 REMARK 3 S TENSOR REMARK 3 S11: 0.2127 S12: -0.1729 S13: -0.0910 REMARK 3 S21: 0.4267 S22: -0.2376 S23: -0.1150 REMARK 3 S31: 0.0524 S32: -0.0156 S33: 0.0433 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 40 THROUGH 64 ) REMARK 3 ORIGIN FOR THE GROUP (A): -18.7745 -13.4875 -15.7198 REMARK 3 T TENSOR REMARK 3 T11: 0.1961 T22: 0.2868 REMARK 3 T33: 0.2612 T12: 0.0133 REMARK 3 T13: 0.0305 T23: -0.0022 REMARK 3 L TENSOR REMARK 3 L11: 2.2575 L22: 5.7737 REMARK 3 L33: 3.5006 L12: 0.5185 REMARK 3 L13: -0.5744 L23: -1.4577 REMARK 3 S TENSOR REMARK 3 S11: 0.1875 S12: 0.2102 S13: 0.1497 REMARK 3 S21: 0.2455 S22: 0.0044 S23: 0.4224 REMARK 3 S31: -0.3333 S32: -0.4194 S33: -0.1969 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 65 THROUGH 176 ) REMARK 3 ORIGIN FOR THE GROUP (A): -7.5717 -20.0820 -12.4313 REMARK 3 T TENSOR REMARK 3 T11: 0.2184 T22: 0.2340 REMARK 3 T33: 0.2597 T12: -0.0469 REMARK 3 T13: -0.0223 T23: 0.0042 REMARK 3 L TENSOR REMARK 3 L11: 1.5540 L22: 1.4791 REMARK 3 L33: 3.3067 L12: 0.5300 REMARK 3 L13: -0.6286 L23: -0.1171 REMARK 3 S TENSOR REMARK 3 S11: 0.1353 S12: -0.1693 S13: -0.0123 REMARK 3 S21: 0.1892 S22: -0.1079 S23: 0.0164 REMARK 3 S31: -0.0023 S32: -0.0090 S33: -0.0247 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 177 THROUGH 205 ) REMARK 3 ORIGIN FOR THE GROUP (A): -7.8100 -1.6457 -27.6958 REMARK 3 T TENSOR REMARK 3 T11: 0.2158 T22: 0.2722 REMARK 3 T33: 0.2226 T12: 0.0446 REMARK 3 T13: 0.0063 T23: 0.0169 REMARK 3 L TENSOR REMARK 3 L11: 1.2904 L22: 3.0717 REMARK 3 L33: 1.6714 L12: 0.8197 REMARK 3 L13: 0.8462 L23: 0.5554 REMARK 3 S TENSOR REMARK 3 S11: -0.1568 S12: -0.0138 S13: 0.1864 REMARK 3 S21: -0.2451 S22: 0.0730 S23: 0.3982 REMARK 3 S31: -0.2185 S32: -0.1966 S33: 0.0751 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 206 THROUGH 268 ) REMARK 3 ORIGIN FOR THE GROUP (A): 3.2090 5.0553 -17.5740 REMARK 3 T TENSOR REMARK 3 T11: 0.2725 T22: 0.2170 REMARK 3 T33: 0.2099 T12: -0.0063 REMARK 3 T13: -0.0006 T23: -0.0331 REMARK 3 L TENSOR REMARK 3 L11: 2.5488 L22: 3.3187 REMARK 3 L33: 2.9559 L12: -0.4505 REMARK 3 L13: 0.2553 L23: 0.4370 REMARK 3 S TENSOR REMARK 3 S11: -0.0998 S12: -0.0893 S13: 0.0845 REMARK 3 S21: 0.1428 S22: 0.0412 S23: 0.1301 REMARK 3 S31: -0.2432 S32: -0.0853 S33: 0.0804 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 269 THROUGH 298 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.7036 -4.2364 -9.7985 REMARK 3 T TENSOR REMARK 3 T11: 0.2949 T22: 0.2147 REMARK 3 T33: 0.2102 T12: -0.0335 REMARK 3 T13: -0.0320 T23: -0.0007 REMARK 3 L TENSOR REMARK 3 L11: 2.9265 L22: 5.5710 REMARK 3 L33: 4.5885 L12: -1.1005 REMARK 3 L13: -0.7308 L23: 1.9303 REMARK 3 S TENSOR REMARK 3 S11: -0.0995 S12: -0.0649 S13: -0.1322 REMARK 3 S21: 0.6184 S22: 0.1036 S23: -0.0753 REMARK 3 S31: 0.3445 S32: 0.1721 S33: -0.0481 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 299 THROUGH 320 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.6450 3.1281 -9.6290 REMARK 3 T TENSOR REMARK 3 T11: 0.3701 T22: 0.2991 REMARK 3 T33: 0.3360 T12: -0.1097 REMARK 3 T13: -0.0965 T23: 0.0174 REMARK 3 L TENSOR REMARK 3 L11: 7.8407 L22: 9.4774 REMARK 3 L33: 9.2365 L12: -1.6181 REMARK 3 L13: -1.3621 L23: 1.3867 REMARK 3 S TENSOR REMARK 3 S11: -0.1642 S12: -0.3531 S13: -0.1310 REMARK 3 S21: 0.7678 S22: 0.2486 S23: -0.7592 REMARK 3 S31: 0.4754 S32: 0.6145 S33: -0.0961 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 5O70 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-JUN-17. REMARK 100 THE DEPOSITION ID IS D_1200005294. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-DEC-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PETRA III, EMBL C/O DESY REMARK 200 BEAMLINE : P13 (MX1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1999 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 106665 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 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 (%) : 99.5 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.7400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.3 REMARK 200 DATA REDUNDANCY IN SHELL : 6.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.670 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 5O4Z REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.2M AMMONIUM SULFATE, 0.1M SODIUM REMARK 280 CITRATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 60.93500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 60.93500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 35.70500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 43.79500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 35.70500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 43.79500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 60.93500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 35.70500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 43.79500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 60.93500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 35.70500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 43.79500 REMARK 290 SMTRY3 8 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 11080 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24630 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -276.0 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -60.93500 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 634 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 674 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 754 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 786 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 789 LIES ON A SPECIAL POSITION. 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 -4 REMARK 465 SER A -3 REMARK 465 GLU A 321 REMARK 465 SER A 322 REMARK 465 GLU A 323 REMARK 465 LYS A 324 REMARK 465 ILE A 325 REMARK 465 PRO A 326 REMARK 465 GLU A 327 REMARK 465 GLY A 328 REMARK 465 ASP A 329 REMARK 465 VAL A 330 REMARK 465 LEU A 331 REMARK 465 GLY A 332 REMARK 465 GLY A 333 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 654 O HOH A 778 1.99 REMARK 500 O2P AMP A 402 O HOH A 501 2.03 REMARK 500 O HOH A 502 O HOH A 503 2.07 REMARK 500 O2' AMP A 401 O HOH A 502 2.11 REMARK 500 O3' AMP A 401 O3P AMP A 402 2.12 REMARK 500 O HOH A 694 O HOH A 776 2.14 REMARK 500 O HOH A 509 O HOH A 547 2.14 REMARK 500 O3P AMP A 402 O HOH A 503 2.15 REMARK 500 O HOH A 717 O HOH A 787 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 704 O HOH A 704 3554 2.09 REMARK 500 O HOH A 525 O HOH A 564 8545 2.14 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 ASN A 70 70.95 51.10 REMARK 500 PRO A 258 -162.41 -70.99 REMARK 500 LYS A 269 -62.85 -96.70 REMARK 500 TRP A 271 -23.73 -147.03 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 794 DISTANCE = 5.94 ANGSTROMS REMARK 525 HOH A 795 DISTANCE = 8.08 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AMP A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AMP A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 410 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 411 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 412 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 413 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 414 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5O25 RELATED DB: PDB REMARK 900 THIS ENTRY CONTAINS T. MARITIMA PDE D80N D154N IN COMPLEX WITH 2 AMP REMARK 900 RELATED ID: 5O4Z RELATED DB: PDB REMARK 900 RELATED ID: 5O58 RELATED DB: PDB REMARK 900 RELATED ID: 5O1U RELATED DB: PDB DBREF 5O70 A 1 333 UNP Q9X1T1 Q9X1T1_THEMA 1 333 SEQADV 5O70 GLY A -4 UNP Q9X1T1 EXPRESSION TAG SEQADV 5O70 SER A -3 UNP Q9X1T1 EXPRESSION TAG SEQADV 5O70 GLY A -2 UNP Q9X1T1 EXPRESSION TAG SEQADV 5O70 SER A -1 UNP Q9X1T1 EXPRESSION TAG SEQADV 5O70 GLY A 0 UNP Q9X1T1 EXPRESSION TAG SEQADV 5O70 ASN A 80 UNP Q9X1T1 ASP 80 ENGINEERED MUTATION SEQADV 5O70 ASN A 154 UNP Q9X1T1 ASP 154 ENGINEERED MUTATION SEQRES 1 A 338 GLY SER GLY SER GLY MET ASP GLU ILE VAL LYS VAL LEU SEQRES 2 A 338 SER GLN HIS ASP ARG ILE LEU VAL VAL GLY HIS ILE MET SEQRES 3 A 338 PRO ASP GLY ASP CYS VAL SER SER VAL LEU SER LEU THR SEQRES 4 A 338 LEU GLY LEU GLU LYS LEU GLY LYS GLU VAL LYS ALA ALA SEQRES 5 A 338 VAL ASP TYR LYS ILE PRO TYR VAL PHE GLU LYS PHE PRO SEQRES 6 A 338 TYR ILE ASP LYS ILE GLU GLU ASN PRO ASN PHE ASP PRO SEQRES 7 A 338 GLU LEU LEU VAL VAL VAL ASN ALA SER SER PRO ASP ARG SEQRES 8 A 338 ILE GLY LYS PHE GLN ASP LEU LEU ASP LYS VAL PRO SER SEQRES 9 A 338 VAL VAL ILE ASP HIS HIS SER THR ASN THR ASN PHE GLY SEQRES 10 A 338 ASN TRP ASN TRP VAL ASP PRO SER PHE ALA ALA THR ALA SEQRES 11 A 338 GLN MET ILE PHE ARG ILE ASN LYS ALA LEU GLY VAL GLU SEQRES 12 A 338 TYR ASP SER ASN LEU ALA THR LEU ASN TYR LEU GLY ILE SEQRES 13 A 338 ALA THR ASN THR GLY PHE PHE ARG HIS SER ASN ALA ASP SEQRES 14 A 338 VAL ARG VAL PHE GLU ASP ALA TYR LYS LEU VAL LYS MET SEQRES 15 A 338 GLY ALA ASP ALA HIS PHE VAL ALA LYS GLU ILE LEU GLU SEQRES 16 A 338 ASN LYS ARG PHE GLU GLN PHE LYS LEU PHE ALA GLU VAL SEQRES 17 A 338 LEU GLU ARG LEU GLN LEU LEU GLU ASN GLY LYS ILE ALA SEQRES 18 A 338 TYR SER TYR ILE ASP TYR ASP THR TYR LEU ARG HIS ASN SEQRES 19 A 338 CYS THR ASP GLU ASP SER ALA GLY PHE VAL GLY GLU LEU SEQRES 20 A 338 ARG SER ILE ARG GLY VAL GLU VAL ALA VAL LEU PHE MET SEQRES 21 A 338 GLU PHE PRO ARG GLY LYS ILE HIS VAL SER MET ARG SER SEQRES 22 A 338 LYS ASP TRP PHE ASN VAL ASN GLU VAL ALA PHE GLU LEU SEQRES 23 A 338 GLY GLY GLY GLY HIS PRO ARG ALA ALA GLY VAL THR PHE SEQRES 24 A 338 GLU GLY LYS LYS ILE GLU GLU VAL ILE PRO ARG VAL ILE SEQRES 25 A 338 ASN HIS LEU LEU LYS LYS PHE LYS GLU GLY VAL GLU SER SEQRES 26 A 338 GLU SER GLU LYS ILE PRO GLU GLY ASP VAL LEU GLY GLY HET AMP A 401 23 HET AMP A 402 23 HET SO4 A 403 5 HET SO4 A 404 5 HET SO4 A 405 5 HET SO4 A 406 5 HET SO4 A 407 5 HET SO4 A 408 5 HET SO4 A 409 5 HET SO4 A 410 5 HET SO4 A 411 5 HET SO4 A 412 5 HET GOL A 413 6 HET GOL A 414 6 HETNAM AMP ADENOSINE MONOPHOSPHATE HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 AMP 2(C10 H14 N5 O7 P) FORMUL 4 SO4 10(O4 S 2-) FORMUL 14 GOL 2(C3 H8 O3) FORMUL 16 HOH *295(H2 O) HELIX 1 AA1 GLY A 0 HIS A 11 1 12 HELIX 2 AA2 ASP A 23 LEU A 40 1 18 HELIX 3 AA3 PRO A 53 GLU A 57 5 5 HELIX 4 AA4 TYR A 61 ASP A 63 5 3 HELIX 5 AA5 SER A 83 LYS A 96 5 14 HELIX 6 AA6 ALA A 123 GLY A 136 1 14 HELIX 7 AA7 ASP A 140 THR A 155 1 16 HELIX 8 AA8 ASP A 164 MET A 177 1 14 HELIX 9 AA9 ASP A 180 GLU A 190 1 11 HELIX 10 AB1 ARG A 193 ARG A 206 1 14 HELIX 11 AB2 ASP A 221 HIS A 228 1 8 HELIX 12 AB3 GLY A 237 SER A 244 1 8 HELIX 13 AB4 ASN A 273 LEU A 281 1 9 HELIX 14 AB5 LYS A 298 SER A 320 1 23 SHEET 1 AA1 6 ILE A 65 GLU A 66 0 SHEET 2 AA1 6 GLU A 43 ALA A 47 1 N ALA A 46 O GLU A 66 SHEET 3 AA1 6 ARG A 13 VAL A 17 1 N VAL A 16 O LYS A 45 SHEET 4 AA1 6 LEU A 75 VAL A 79 1 O VAL A 77 N LEU A 15 SHEET 5 AA1 6 SER A 99 ASP A 103 1 O VAL A 100 N VAL A 78 SHEET 6 AA1 6 TRP A 114 VAL A 117 1 O TRP A 116 N VAL A 101 SHEET 1 AA2 6 GLN A 208 LEU A 210 0 SHEET 2 AA2 6 ILE A 215 ILE A 220 -1 O TYR A 217 N GLN A 208 SHEET 3 AA2 6 VAL A 250 GLU A 256 1 O GLU A 256 N ILE A 220 SHEET 4 AA2 6 LYS A 261 SER A 268 -1 O HIS A 263 N MET A 255 SHEET 5 AA2 6 ALA A 289 GLU A 295 -1 O VAL A 292 N VAL A 264 SHEET 6 AA2 6 GLY A 284 HIS A 286 -1 N HIS A 286 O ALA A 289 CISPEP 1 PHE A 257 PRO A 258 0 -8.28 SITE 1 AC1 23 HIS A 263 SER A 265 ARG A 267 GLY A 283 SITE 2 AC1 23 GLY A 284 GLY A 285 HIS A 286 ALA A 289 SITE 3 AC1 23 ALA A 290 GLY A 291 VAL A 292 THR A 293 SITE 4 AC1 23 AMP A 402 GOL A 413 HOH A 502 HOH A 503 SITE 5 AC1 23 HOH A 516 HOH A 532 HOH A 585 HOH A 621 SITE 6 AC1 23 HOH A 636 HOH A 637 HOH A 671 SITE 1 AC2 17 HIS A 104 HIS A 105 THR A 153 ASN A 154 SITE 2 AC2 17 HIS A 160 SER A 161 ASN A 162 ARG A 267 SITE 3 AC2 17 HIS A 286 ARG A 288 ALA A 289 AMP A 401 SITE 4 AC2 17 SO4 A 407 HOH A 501 HOH A 503 HOH A 517 SITE 5 AC2 17 HOH A 625 SITE 1 AC3 4 GLU A 66 GLU A 67 ASN A 68 HOH A 648 SITE 1 AC4 3 ARG A 130 ARG A 166 HOH A 688 SITE 1 AC5 3 ASP A 140 SER A 141 HOH A 523 SITE 1 AC6 4 LYS A 192 PHE A 200 GLU A 241 HOH A 704 SITE 1 AC7 8 HIS A 160 GLY A 237 GLY A 240 ARG A 243 SITE 2 AC7 8 ARG A 267 AMP A 402 HOH A 513 HOH A 609 SITE 1 AC8 7 LEU A 281 GLY A 282 VAL A 292 THR A 293 SITE 2 AC8 7 PHE A 294 HOH A 657 HOH A 697 SITE 1 AC9 8 TYR A 54 ARG A 193 ARG A 246 HOH A 529 SITE 2 AC9 8 HOH A 565 HOH A 570 HOH A 603 HOH A 685 SITE 1 AD1 5 GLU A 280 ARG A 305 HIS A 309 HOH A 525 SITE 2 AD1 5 HOH A 684 SITE 1 AD2 5 SER A -1 GLY A -2 ASN A 113 TRP A 114 SITE 2 AD2 5 ASN A 115 SITE 1 AD3 7 SER A 106 PRO A 119 GLY A 285 HIS A 286 SITE 2 AD3 7 PRO A 287 HOH A 592 HOH A 629 SITE 1 AD4 5 ARG A 86 HIS A 263 AMP A 401 HOH A 502 SITE 2 AD4 5 HOH A 516 SITE 1 AD5 5 TYR A 219 GLU A 300 HOH A 515 HOH A 590 SITE 2 AD5 5 HOH A 672 CRYST1 71.410 87.590 121.870 90.00 90.00 90.00 C 2 2 21 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 0.014004 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011417 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008205 0.00000