HEADER OXIDOREDUCTASE 29-NOV-17 6F4O TITLE HUMAN JMJD5 IN COMPLEX WITH MN(II) AND SUCCINATE. COMPND MOL_ID: 1; COMPND 2 MOLECULE: JMJC DOMAIN-CONTAINING PROTEIN 5; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: JMJC DOMAIN-CONTAINING PROTEIN 5,JUMONJI DOMAIN-CONTAINING COMPND 5 PROTEIN 5; COMPND 6 EC: 1.14.11.47; COMPND 7 ENGINEERED: YES; COMPND 8 OTHER_DETAILS: CATALYTIC DOMAIN (RESIDUES 183-416) SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: KDM8, JMJD5; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PNIC28 BSA4 KEYWDS OXIDOREDUCTASE, NON-HEME, IRON, 2-OXOGLUTARATE, DIOXYGENASE, JMJC, KEYWDS 2 JMJC DOMAIN, LYSINE-SPECIFIC DEMETHYLASE 8, JMJC DOMAIN-CONTAINING KEYWDS 3 PROTEIN 5, ARGINYL C-3 HYDROXYLASE, JMJD5, KDM8, OXYGENASE, HYPOXIA, KEYWDS 4 DNA-BINDING, METAL-BINDING, TRANSLATION, DSBH, FACIAL TRIAD, KEYWDS 5 CYTOPLASM, JMJC HYDROXYLASE, JMJC DEMETHYLASE, KDMS, POST- KEYWDS 6 TRANSLATIONAL MODIFICATIONS, PTM, BETA-HYDROXYLATION, HYDROXYLATION, KEYWDS 7 ARGININE HYDROXYLATION, RCC1 DOMAIN-CONTAINING PROTEIN 1, RCCD1, KEYWDS 8 REGULATOR OF CHROMOSOME CONDENSATION, 40S RIBOSOMAL PROTEIN S6, KEYWDS 9 RPS6, RIBOSOME BIOGENESIS, TRANSCRIPTION, EPIGENETIC REGULATION, KEYWDS 10 SIGNALING, DEVELOPMENT, CELL STRUCTURE, TRANSCRIPTION KEYWDS 11 ACTIVATOR/INHIBITOR, PHOSPHORYLATION, CANCER, POLYMORPHISM EXPDTA X-RAY DIFFRACTION AUTHOR R.CHOWDHURY,M.S.ISLAM,C.J.SCHOFIELD REVDAT 2 17-JAN-24 6F4O 1 LINK REVDAT 1 04-APR-18 6F4O 0 JRNL AUTH S.E.WILKINS,S.ISLAM,J.M.GANNON,S.MARKOLOVIC,R.J.HOPKINSON, JRNL AUTH 2 W.GE,C.J.SCHOFIELD,R.CHOWDHURY JRNL TITL JMJD5 IS A HUMAN ARGINYL C-3 HYDROXYLASE. JRNL REF NAT COMMUN V. 9 1180 2018 JRNL REFN ESSN 2041-1723 JRNL PMID 29563586 JRNL DOI 10.1038/S41467-018-03410-W REMARK 2 REMARK 2 RESOLUTION. 1.28 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) : 1.28 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.56 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 64244 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.147 REMARK 3 R VALUE (WORKING SET) : 0.146 REMARK 3 FREE R VALUE : 0.174 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 3259 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 27.5683 - 3.6375 0.97 2780 134 0.1512 0.1988 REMARK 3 2 3.6375 - 2.8882 0.99 2704 132 0.1368 0.1645 REMARK 3 3 2.8882 - 2.5234 0.99 2712 143 0.1404 0.1742 REMARK 3 4 2.5234 - 2.2928 1.00 2682 124 0.1350 0.1537 REMARK 3 5 2.2928 - 2.1285 1.00 2688 147 0.1261 0.1504 REMARK 3 6 2.1285 - 2.0031 1.00 2675 122 0.1203 0.1376 REMARK 3 7 2.0031 - 1.9028 1.00 2618 161 0.1186 0.1275 REMARK 3 8 1.9028 - 1.8200 1.00 2696 135 0.1268 0.1631 REMARK 3 9 1.8200 - 1.7499 1.00 2646 136 0.1274 0.1577 REMARK 3 10 1.7499 - 1.6895 1.00 2651 152 0.1371 0.1457 REMARK 3 11 1.6895 - 1.6367 1.00 2637 146 0.1390 0.1773 REMARK 3 12 1.6367 - 1.5899 1.00 2631 141 0.1434 0.1616 REMARK 3 13 1.5899 - 1.5481 1.00 2618 154 0.1505 0.1871 REMARK 3 14 1.5481 - 1.5103 1.00 2639 140 0.1524 0.1697 REMARK 3 15 1.5103 - 1.4760 1.00 2637 142 0.1630 0.1868 REMARK 3 16 1.4760 - 1.4446 1.00 2638 134 0.1746 0.2035 REMARK 3 17 1.4446 - 1.4157 1.00 2629 149 0.1946 0.2135 REMARK 3 18 1.4157 - 1.3890 1.00 2621 150 0.2117 0.2614 REMARK 3 19 1.3890 - 1.3642 1.00 2613 145 0.2217 0.2502 REMARK 3 20 1.3642 - 1.3410 1.00 2618 137 0.2332 0.2103 REMARK 3 21 1.3410 - 1.3194 1.00 2633 141 0.2459 0.2732 REMARK 3 22 1.3194 - 1.2991 1.00 2620 145 0.2541 0.2583 REMARK 3 23 1.2991 - 1.2800 0.99 2599 149 0.2645 0.2711 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.40 REMARK 3 B_SOL : 51.60 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.270 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.87000 REMARK 3 B22 (A**2) : -1.23000 REMARK 3 B33 (A**2) : 5.09000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : 0.011 2219 REMARK 3 ANGLE : 1.121 3057 REMARK 3 CHIRALITY : 0.086 313 REMARK 3 PLANARITY : 0.009 413 REMARK 3 DIHEDRAL : 14.064 831 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 12 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID 182:211) REMARK 3 ORIGIN FOR THE GROUP (A): -24.2560 22.9473 -20.3272 REMARK 3 T TENSOR REMARK 3 T11: 0.1690 T22: 0.2118 REMARK 3 T33: 0.2150 T12: 0.0534 REMARK 3 T13: 0.0418 T23: 0.0424 REMARK 3 L TENSOR REMARK 3 L11: 1.1649 L22: 0.7728 REMARK 3 L33: 1.5104 L12: -0.5677 REMARK 3 L13: -0.0613 L23: 0.1594 REMARK 3 S TENSOR REMARK 3 S11: 0.0468 S12: 0.0401 S13: 0.2308 REMARK 3 S21: 0.0601 S22: 0.1300 S23: 0.2046 REMARK 3 S31: -0.3182 S32: -0.3771 S33: 0.0698 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 212:230) REMARK 3 ORIGIN FOR THE GROUP (A): -8.2888 10.8291 -2.8306 REMARK 3 T TENSOR REMARK 3 T11: 0.2608 T22: 0.2592 REMARK 3 T33: 0.1510 T12: 0.0396 REMARK 3 T13: 0.0096 T23: -0.0212 REMARK 3 L TENSOR REMARK 3 L11: 0.1706 L22: 0.2737 REMARK 3 L33: 0.5538 L12: 0.1827 REMARK 3 L13: -0.0415 L23: -0.2077 REMARK 3 S TENSOR REMARK 3 S11: -0.1649 S12: -0.1994 S13: 0.1111 REMARK 3 S21: 0.2454 S22: 0.2326 S23: -0.1071 REMARK 3 S31: -0.1408 S32: -0.0421 S33: -0.0001 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 231:254) REMARK 3 ORIGIN FOR THE GROUP (A): 2.5328 1.7276 -17.0819 REMARK 3 T TENSOR REMARK 3 T11: 0.2224 T22: 0.1881 REMARK 3 T33: 0.1768 T12: 0.0297 REMARK 3 T13: 0.0351 T23: 0.0124 REMARK 3 L TENSOR REMARK 3 L11: 0.6779 L22: 0.8188 REMARK 3 L33: 0.2609 L12: -0.5181 REMARK 3 L13: 0.2290 L23: 0.1928 REMARK 3 S TENSOR REMARK 3 S11: 0.1037 S12: 0.1585 S13: -0.0887 REMARK 3 S21: -0.1965 S22: -0.0789 S23: -0.1154 REMARK 3 S31: 0.0867 S32: 0.1354 S33: -0.0002 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN A AND RESID 255:277) REMARK 3 ORIGIN FOR THE GROUP (A): 5.5469 8.1526 -13.9042 REMARK 3 T TENSOR REMARK 3 T11: 0.1527 T22: 0.1963 REMARK 3 T33: 0.2151 T12: -0.0066 REMARK 3 T13: 0.0006 T23: 0.0317 REMARK 3 L TENSOR REMARK 3 L11: 0.5937 L22: 1.1387 REMARK 3 L33: 1.2441 L12: -0.9040 REMARK 3 L13: 0.0912 L23: -0.6127 REMARK 3 S TENSOR REMARK 3 S11: 0.0380 S12: 0.2037 S13: 0.1225 REMARK 3 S21: 0.0789 S22: -0.1463 S23: -0.2374 REMARK 3 S31: 0.0046 S32: 0.3156 S33: -0.0011 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN A AND RESID 278:305) REMARK 3 ORIGIN FOR THE GROUP (A): -19.4401 4.8632 -12.4668 REMARK 3 T TENSOR REMARK 3 T11: 0.2117 T22: 0.2216 REMARK 3 T33: 0.3027 T12: -0.0167 REMARK 3 T13: 0.0294 T23: 0.0631 REMARK 3 L TENSOR REMARK 3 L11: 0.5021 L22: 0.5406 REMARK 3 L33: 0.2128 L12: -0.2219 REMARK 3 L13: -0.1462 L23: -0.5490 REMARK 3 S TENSOR REMARK 3 S11: -0.1129 S12: -0.0719 S13: -0.3136 REMARK 3 S21: 0.0622 S22: 0.1355 S23: 0.2535 REMARK 3 S31: 0.1416 S32: -0.2269 S33: 0.0056 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN A AND RESID 306:312) REMARK 3 ORIGIN FOR THE GROUP (A): -8.4416 7.9174 -16.2482 REMARK 3 T TENSOR REMARK 3 T11: 0.1454 T22: 0.1276 REMARK 3 T33: 0.1835 T12: 0.0007 REMARK 3 T13: -0.0102 T23: -0.0059 REMARK 3 L TENSOR REMARK 3 L11: 0.0721 L22: 0.0676 REMARK 3 L33: 0.1310 L12: -0.0090 REMARK 3 L13: -0.0009 L23: -0.1505 REMARK 3 S TENSOR REMARK 3 S11: -0.0837 S12: -0.0470 S13: 0.1400 REMARK 3 S21: -0.0886 S22: 0.0698 S23: 0.1639 REMARK 3 S31: -0.0006 S32: 0.0422 S33: -0.0000 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: (CHAIN A AND RESID 313:325) REMARK 3 ORIGIN FOR THE GROUP (A): -7.2306 13.3289 -26.1072 REMARK 3 T TENSOR REMARK 3 T11: 0.1416 T22: 0.1338 REMARK 3 T33: 0.1481 T12: 0.0004 REMARK 3 T13: -0.0156 T23: -0.0174 REMARK 3 L TENSOR REMARK 3 L11: 0.0626 L22: 0.0912 REMARK 3 L33: 0.6760 L12: 0.0089 REMARK 3 L13: -0.1276 L23: -0.3097 REMARK 3 S TENSOR REMARK 3 S11: 0.0772 S12: 0.0371 S13: -0.0938 REMARK 3 S21: 0.0222 S22: -0.0128 S23: -0.0402 REMARK 3 S31: 0.0917 S32: 0.0671 S33: -0.0002 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: (CHAIN A AND RESID 326:341) REMARK 3 ORIGIN FOR THE GROUP (A): -10.3244 18.7903 -19.8255 REMARK 3 T TENSOR REMARK 3 T11: 0.1473 T22: 0.1231 REMARK 3 T33: 0.1321 T12: 0.0031 REMARK 3 T13: 0.0042 T23: -0.0003 REMARK 3 L TENSOR REMARK 3 L11: 0.2548 L22: 0.1751 REMARK 3 L33: 0.3827 L12: -0.2248 REMARK 3 L13: -0.1849 L23: -0.2206 REMARK 3 S TENSOR REMARK 3 S11: 0.0093 S12: -0.0370 S13: 0.0143 REMARK 3 S21: 0.0770 S22: 0.0492 S23: 0.0281 REMARK 3 S31: -0.0883 S32: 0.0144 S33: -0.0000 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: (CHAIN A AND RESID 342:365) REMARK 3 ORIGIN FOR THE GROUP (A): -8.0116 14.0911 -37.2945 REMARK 3 T TENSOR REMARK 3 T11: 0.2022 T22: 0.1978 REMARK 3 T33: 0.2075 T12: -0.0126 REMARK 3 T13: 0.0152 T23: -0.0473 REMARK 3 L TENSOR REMARK 3 L11: 0.8149 L22: 0.3516 REMARK 3 L33: 1.2868 L12: -0.0226 REMARK 3 L13: -0.8328 L23: -0.5390 REMARK 3 S TENSOR REMARK 3 S11: -0.0449 S12: 0.3156 S13: -0.3847 REMARK 3 S21: -0.1931 S22: -0.0071 S23: -0.0281 REMARK 3 S31: 0.0996 S32: -0.0346 S33: 0.0000 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: (CHAIN A AND RESID 366:381) REMARK 3 ORIGIN FOR THE GROUP (A): -2.0198 24.5820 -39.1507 REMARK 3 T TENSOR REMARK 3 T11: 0.2116 T22: 0.2151 REMARK 3 T33: 0.1627 T12: 0.0204 REMARK 3 T13: 0.0605 T23: 0.0079 REMARK 3 L TENSOR REMARK 3 L11: 0.2338 L22: 0.4599 REMARK 3 L33: 0.2086 L12: 0.1563 REMARK 3 L13: -0.2619 L23: -0.0117 REMARK 3 S TENSOR REMARK 3 S11: 0.2062 S12: 0.1304 S13: 0.1376 REMARK 3 S21: -0.0634 S22: -0.0145 S23: -0.1283 REMARK 3 S31: -0.2739 S32: 0.0586 S33: 0.0060 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: (CHAIN A AND RESID 382:399) REMARK 3 ORIGIN FOR THE GROUP (A): -14.4820 19.5510 -22.6624 REMARK 3 T TENSOR REMARK 3 T11: 0.1451 T22: 0.1389 REMARK 3 T33: 0.1395 T12: 0.0100 REMARK 3 T13: 0.0084 T23: -0.0088 REMARK 3 L TENSOR REMARK 3 L11: 0.4949 L22: 0.2310 REMARK 3 L33: 0.4387 L12: 0.0354 REMARK 3 L13: -0.3809 L23: -0.4549 REMARK 3 S TENSOR REMARK 3 S11: 0.0080 S12: 0.0148 S13: 0.0526 REMARK 3 S21: 0.0541 S22: 0.0550 S23: 0.0726 REMARK 3 S31: -0.1347 S32: -0.0581 S33: 0.0000 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: (CHAIN A AND RESID 400:416) REMARK 3 ORIGIN FOR THE GROUP (A): -10.6225 13.3781 -19.2494 REMARK 3 T TENSOR REMARK 3 T11: 0.1378 T22: 0.1277 REMARK 3 T33: 0.1432 T12: -0.0036 REMARK 3 T13: -0.0075 T23: -0.0056 REMARK 3 L TENSOR REMARK 3 L11: 0.2463 L22: 0.6067 REMARK 3 L33: 0.9551 L12: -0.2046 REMARK 3 L13: -0.3935 L23: -0.4155 REMARK 3 S TENSOR REMARK 3 S11: -0.0082 S12: 0.0363 S13: -0.0731 REMARK 3 S21: 0.0549 S22: 0.0395 S23: 0.0046 REMARK 3 S31: -0.0135 S32: -0.0434 S33: -0.0000 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT TARGET : ML AND BULK SOLVENT REMARK 3 MODELLING METHOD USED : FLAT MODEL REMARK 4 REMARK 4 6F4O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-NOV-17. REMARK 100 THE DEPOSITION ID IS D_1200007738. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JAN-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 706E REMARK 200 DATA SCALING SOFTWARE : HKL-2000 706E REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 64327 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.280 REMARK 200 RESOLUTION RANGE LOW (A) : 27.560 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.08100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.28 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.33 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.40 REMARK 200 R MERGE FOR SHELL (I) : 1.10000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 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: 4GJZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS PH 6.5, 15.0 % PEG3350, REMARK 280 0.002 M MNCL2, 300 NL SITTING DROPS (SAMPLE:WELL, 2:1 RATIO), REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K 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 24.71700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 38.74550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.20550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.74550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.71700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.20550 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 700 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11400 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -2.0 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 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 HIS A 162 REMARK 465 HIS A 163 REMARK 465 HIS A 164 REMARK 465 HIS A 165 REMARK 465 HIS A 166 REMARK 465 HIS A 167 REMARK 465 SER A 168 REMARK 465 SER A 169 REMARK 465 GLY A 170 REMARK 465 VAL A 171 REMARK 465 ASP A 172 REMARK 465 LEU A 173 REMARK 465 GLY A 174 REMARK 465 THR A 175 REMARK 465 GLU A 176 REMARK 465 ASN A 177 REMARK 465 LEU A 178 REMARK 465 TYR A 179 REMARK 465 PHE A 180 REMARK 465 GLN A 181 REMARK 465 SER A 241 REMARK 465 ARG A 242 REMARK 465 TYR A 243 REMARK 465 THR A 244 REMARK 465 ASP A 245 REMARK 465 GLU A 246 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 247 CG CD OE1 OE2 REMARK 470 ASP A 353 CG OD1 OD2 REMARK 470 LYS A 378 CG CD CE NZ 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 189 61.62 35.03 REMARK 500 PHE A 199 -52.73 -131.74 REMARK 500 GLU A 266 98.00 -53.24 REMARK 500 ASN A 367 67.69 -150.64 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 501 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 321 NE2 REMARK 620 2 ASP A 323 OD2 111.4 REMARK 620 3 HIS A 400 NE2 87.6 82.7 REMARK 620 4 SIN A 502 O3 80.3 168.3 98.8 REMARK 620 5 SIN A 502 O4 135.7 112.4 92.4 56.0 REMARK 620 6 HOH A 684 O 90.4 85.5 166.4 94.1 98.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 501 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 321 NE2 REMARK 620 2 ASP A 323 OD1 77.5 REMARK 620 3 ASP A 323 OD2 129.7 53.5 REMARK 620 4 HIS A 400 NE2 79.6 89.9 88.8 REMARK 620 5 SIN A 502 O3 96.1 173.0 133.3 91.8 REMARK 620 6 HOH A 611 O 166.8 94.7 46.5 111.4 90.9 REMARK 620 7 HOH A 684 O 96.9 85.6 90.6 174.8 92.4 71.7 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SIN A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TRS A 503 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6F4M RELATED DB: PDB REMARK 900 RELATED ID: 6F4N RELATED DB: PDB REMARK 900 RELATED ID: 6F4P RELATED DB: PDB REMARK 900 RELATED ID: 6F4Q RELATED DB: PDB REMARK 900 RELATED ID: 6F4R RELATED DB: PDB REMARK 900 RELATED ID: 6F4S RELATED DB: PDB REMARK 900 RELATED ID: 6F4T RELATED DB: PDB DBREF 6F4O A 183 416 UNP Q8N371 KDM8_HUMAN 183 416 SEQADV 6F4O HIS A 162 UNP Q8N371 EXPRESSION TAG SEQADV 6F4O HIS A 163 UNP Q8N371 EXPRESSION TAG SEQADV 6F4O HIS A 164 UNP Q8N371 EXPRESSION TAG SEQADV 6F4O HIS A 165 UNP Q8N371 EXPRESSION TAG SEQADV 6F4O HIS A 166 UNP Q8N371 EXPRESSION TAG SEQADV 6F4O HIS A 167 UNP Q8N371 EXPRESSION TAG SEQADV 6F4O SER A 168 UNP Q8N371 EXPRESSION TAG SEQADV 6F4O SER A 169 UNP Q8N371 EXPRESSION TAG SEQADV 6F4O GLY A 170 UNP Q8N371 EXPRESSION TAG SEQADV 6F4O VAL A 171 UNP Q8N371 EXPRESSION TAG SEQADV 6F4O ASP A 172 UNP Q8N371 EXPRESSION TAG SEQADV 6F4O LEU A 173 UNP Q8N371 EXPRESSION TAG SEQADV 6F4O GLY A 174 UNP Q8N371 EXPRESSION TAG SEQADV 6F4O THR A 175 UNP Q8N371 EXPRESSION TAG SEQADV 6F4O GLU A 176 UNP Q8N371 EXPRESSION TAG SEQADV 6F4O ASN A 177 UNP Q8N371 EXPRESSION TAG SEQADV 6F4O LEU A 178 UNP Q8N371 EXPRESSION TAG SEQADV 6F4O TYR A 179 UNP Q8N371 EXPRESSION TAG SEQADV 6F4O PHE A 180 UNP Q8N371 EXPRESSION TAG SEQADV 6F4O GLN A 181 UNP Q8N371 EXPRESSION TAG SEQADV 6F4O SER A 182 UNP Q8N371 EXPRESSION TAG SEQRES 1 A 255 HIS HIS HIS HIS HIS HIS SER SER GLY VAL ASP LEU GLY SEQRES 2 A 255 THR GLU ASN LEU TYR PHE GLN SER THR VAL PRO ARG LEU SEQRES 3 A 255 HIS ARG PRO SER LEU GLN HIS PHE ARG GLU GLN PHE LEU SEQRES 4 A 255 VAL PRO GLY ARG PRO VAL ILE LEU LYS GLY VAL ALA ASP SEQRES 5 A 255 HIS TRP PRO CYS MET GLN LYS TRP SER LEU GLU TYR ILE SEQRES 6 A 255 GLN GLU ILE ALA GLY CYS ARG THR VAL PRO VAL GLU VAL SEQRES 7 A 255 GLY SER ARG TYR THR ASP GLU GLU TRP SER GLN THR LEU SEQRES 8 A 255 MET THR VAL ASN GLU PHE ILE SER LYS TYR ILE VAL ASN SEQRES 9 A 255 GLU PRO ARG ASP VAL GLY TYR LEU ALA GLN HIS GLN LEU SEQRES 10 A 255 PHE ASP GLN ILE PRO GLU LEU LYS GLN ASP ILE SER ILE SEQRES 11 A 255 PRO ASP TYR CYS SER LEU GLY ASP GLY GLU GLU GLU GLU SEQRES 12 A 255 ILE THR ILE ASN ALA TRP PHE GLY PRO GLN GLY THR ILE SEQRES 13 A 255 SER PRO LEU HIS GLN ASP PRO GLN GLN ASN PHE LEU VAL SEQRES 14 A 255 GLN VAL MET GLY ARG LYS TYR ILE ARG LEU TYR SER PRO SEQRES 15 A 255 GLN GLU SER GLY ALA LEU TYR PRO HIS ASP THR HIS LEU SEQRES 16 A 255 LEU HIS ASN THR SER GLN VAL ASP VAL GLU ASN PRO ASP SEQRES 17 A 255 LEU GLU LYS PHE PRO LYS PHE ALA LYS ALA PRO PHE LEU SEQRES 18 A 255 SER CYS ILE LEU SER PRO GLY GLU ILE LEU PHE ILE PRO SEQRES 19 A 255 VAL LYS TYR TRP HIS TYR VAL ARG ALA LEU ASP LEU SER SEQRES 20 A 255 PHE SER VAL SER PHE TRP TRP SER HET MN A 501 2 HET SIN A 502 24 HET TRS A 503 20 HETNAM MN MANGANESE (II) ION HETNAM SIN SUCCINIC ACID HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETSYN TRS TRIS BUFFER FORMUL 2 MN MN 2+ FORMUL 3 SIN C4 H6 O4 FORMUL 4 TRS C4 H12 N O3 1+ FORMUL 5 HOH *303(H2 O) HELIX 1 AA1 SER A 191 PHE A 199 1 9 HELIX 2 AA2 TRP A 215 TRP A 221 1 7 HELIX 3 AA3 SER A 222 GLY A 231 1 10 HELIX 4 AA4 VAL A 255 ILE A 263 1 9 HELIX 5 AA5 GLN A 277 ILE A 282 1 6 HELIX 6 AA6 ILE A 282 GLN A 287 1 6 HELIX 7 AA7 PRO A 292 GLY A 298 5 7 HELIX 8 AA8 GLU A 301 ILE A 305 5 5 HELIX 9 AA9 SER A 342 LEU A 349 5 8 HELIX 10 AB1 THR A 354 HIS A 358 5 5 HELIX 11 AB2 PHE A 373 ALA A 377 5 5 SHEET 1 AA1 9 ARG A 186 HIS A 188 0 SHEET 2 AA1 9 VAL A 206 LYS A 209 1 O LYS A 209 N LEU A 187 SHEET 3 AA1 9 ILE A 391 ILE A 394 -1 O PHE A 393 N VAL A 206 SHEET 4 AA1 9 GLN A 326 MET A 333 -1 N LEU A 329 O LEU A 392 SHEET 5 AA1 9 SER A 408 TRP A 415 -1 O VAL A 411 N VAL A 330 SHEET 6 AA1 9 THR A 306 GLY A 312 -1 N GLY A 312 O SER A 408 SHEET 7 AA1 9 GLY A 271 HIS A 276 -1 N HIS A 276 O ALA A 309 SHEET 8 AA1 9 THR A 234 VAL A 239 -1 N GLU A 238 O TYR A 272 SHEET 9 AA1 9 SER A 249 THR A 254 -1 O MET A 253 N VAL A 235 SHEET 1 AA2 4 ILE A 317 HIS A 321 0 SHEET 2 AA2 4 TRP A 399 ALA A 404 -1 O VAL A 402 N SER A 318 SHEET 3 AA2 4 LYS A 336 TYR A 341 -1 N TYR A 337 O ARG A 403 SHEET 4 AA2 4 LEU A 382 LEU A 386 -1 O LEU A 386 N LYS A 336 LINK NE2 HIS A 321 MN A MN A 501 1555 1555 2.07 LINK NE2 HIS A 321 MN B MN A 501 1555 1555 2.52 LINK OD1BASP A 323 MN B MN A 501 1555 1555 2.51 LINK OD2AASP A 323 MN A MN A 501 1555 1555 2.06 LINK OD2BASP A 323 MN B MN A 501 1555 1555 2.30 LINK NE2 HIS A 400 MN A MN A 501 1555 1555 2.30 LINK NE2 HIS A 400 MN B MN A 501 1555 1555 2.21 LINK MN A MN A 501 O3 ASIN A 502 1555 1555 2.29 LINK MN A MN A 501 O4 ASIN A 502 1555 1555 2.27 LINK MN B MN A 501 O3 BSIN A 502 1555 1555 2.06 LINK MN B MN A 501 O BHOH A 611 1555 1555 2.37 LINK MN A MN A 501 O AHOH A 684 1555 1555 2.22 LINK MN B MN A 501 O BHOH A 684 1555 1555 2.16 SITE 1 AC1 6 HIS A 321 ASP A 323 HIS A 400 SIN A 502 SITE 2 AC1 6 HOH A 611 HOH A 684 SITE 1 AC2 15 TYR A 272 TRP A 310 SER A 318 HIS A 321 SITE 2 AC2 15 ASP A 323 ASN A 327 LYS A 336 HIS A 400 SITE 3 AC2 15 VAL A 402 MN A 501 HOH A 608 HOH A 611 SITE 4 AC2 15 HOH A 684 HOH A 702 HOH A 742 SITE 1 AC3 12 LEU A 200 VAL A 201 GLY A 203 GLN A 326 SITE 2 AC3 12 TYR A 350 LYS A 372 PHE A 373 VAL A 396 SITE 3 AC3 12 HOH A 602 HOH A 605 HOH A 619 HOH A 634 CRYST1 49.434 64.411 77.491 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 0.020229 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015525 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012905 0.00000