HEADER OXIDOREDUCTASE 29-NOV-17 6F4Q TITLE HUMAN JMJD5 (Q275C) IN COMPLEX WITH MN(II), NOG AND RPS6-A138C (129- TITLE 2 144) (COMPLEX-2) COMPND MOL_ID: 1; COMPND 2 MOLECULE: JMJC DOMAIN-CONTAINING PROTEIN 5; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: LYSINE-SPECIFIC DEMETHYLASE 8, JUMONJI DOMAIN-CONTAINING COMPND 5 PROTEIN 5; COMPND 6 EC: 1.14.11.47; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 OTHER_DETAILS: CATALYTIC DOMAIN (RESIDUES 183-416); COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: 40S RIBOSOMAL PROTEIN S6; COMPND 12 CHAIN: B; COMPND 13 SYNONYM: PHOSPHOPROTEIN NP33,SMALL RIBOSOMAL SUBUNIT PROTEIN ES6; COMPND 14 ENGINEERED: YES; COMPND 15 MUTATION: YES; COMPND 16 OTHER_DETAILS: FRAGMENT: 129-144 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; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606 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 6F4Q 1 LINK REVDAT 1 04-APR-18 6F4Q 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. 1.12 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.12 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.91 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 95617 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.140 REMARK 3 R VALUE (WORKING SET) : 0.139 REMARK 3 FREE R VALUE : 0.153 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 4770 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 49.9561 - 3.4807 1.00 3295 179 0.1410 0.1657 REMARK 3 2 3.4807 - 2.7628 1.00 3148 185 0.1253 0.1426 REMARK 3 3 2.7628 - 2.4136 1.00 3102 180 0.1304 0.1445 REMARK 3 4 2.4136 - 2.1929 1.00 3125 165 0.1256 0.1334 REMARK 3 5 2.1929 - 2.0357 1.00 3099 160 0.1228 0.1426 REMARK 3 6 2.0357 - 1.9157 1.00 3072 160 0.1186 0.1362 REMARK 3 7 1.9157 - 1.8197 1.00 3094 155 0.1283 0.1502 REMARK 3 8 1.8197 - 1.7405 1.00 3057 155 0.1307 0.1324 REMARK 3 9 1.7405 - 1.6735 1.00 3061 174 0.1251 0.1429 REMARK 3 10 1.6735 - 1.6158 0.99 3057 144 0.1315 0.1416 REMARK 3 11 1.6158 - 1.5652 1.00 3051 172 0.1280 0.1487 REMARK 3 12 1.5652 - 1.5205 0.99 3030 161 0.1350 0.1320 REMARK 3 13 1.5205 - 1.4805 0.99 3025 155 0.1312 0.1383 REMARK 3 14 1.4805 - 1.4443 0.99 2998 177 0.1358 0.1437 REMARK 3 15 1.4443 - 1.4115 0.99 3004 170 0.1458 0.1645 REMARK 3 16 1.4115 - 1.3815 0.99 3025 169 0.1497 0.1347 REMARK 3 17 1.3815 - 1.3538 0.99 3011 162 0.1541 0.1551 REMARK 3 18 1.3538 - 1.3283 0.99 2995 151 0.1577 0.1724 REMARK 3 19 1.3283 - 1.3046 0.98 3005 170 0.1595 0.1543 REMARK 3 20 1.3046 - 1.2824 0.98 2983 150 0.1619 0.1794 REMARK 3 21 1.2824 - 1.2617 0.98 3013 131 0.1705 0.1555 REMARK 3 22 1.2617 - 1.2423 0.98 2996 132 0.1767 0.1809 REMARK 3 23 1.2423 - 1.2241 0.98 3019 140 0.1876 0.2394 REMARK 3 24 1.2241 - 1.2068 0.98 2922 168 0.1902 0.2124 REMARK 3 25 1.2068 - 1.1905 0.98 3006 154 0.1878 0.1890 REMARK 3 26 1.1905 - 1.1750 0.98 2944 154 0.2041 0.2099 REMARK 3 27 1.1750 - 1.1604 0.98 2947 175 0.2106 0.2466 REMARK 3 28 1.1604 - 1.1464 0.97 2941 146 0.2363 0.2574 REMARK 3 29 1.1464 - 1.1330 0.96 2948 128 0.2568 0.2614 REMARK 3 30 1.1330 - 1.1203 0.94 2874 148 0.2870 0.2545 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.40 REMARK 3 B_SOL : 54.50 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.100 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.030 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.48000 REMARK 3 B22 (A**2) : -0.11000 REMARK 3 B33 (A**2) : 1.60000 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 : 0.010 2322 REMARK 3 ANGLE : 1.162 3196 REMARK 3 CHIRALITY : 0.086 325 REMARK 3 PLANARITY : 0.009 431 REMARK 3 DIHEDRAL : 14.967 879 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): 24.8017 -22.4386 -19.9476 REMARK 3 T TENSOR REMARK 3 T11: 0.1392 T22: 0.1991 REMARK 3 T33: 0.1820 T12: 0.0482 REMARK 3 T13: -0.0321 T23: -0.0313 REMARK 3 L TENSOR REMARK 3 L11: 0.3314 L22: 0.3150 REMARK 3 L33: 0.3302 L12: -0.2065 REMARK 3 L13: 0.0393 L23: -0.0110 REMARK 3 S TENSOR REMARK 3 S11: -0.0043 S12: -0.0030 S13: -0.2001 REMARK 3 S21: 0.0592 S22: 0.0842 S23: -0.1596 REMARK 3 S31: 0.1962 S32: 0.2841 S33: 0.0609 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 212:230) REMARK 3 ORIGIN FOR THE GROUP (A): 8.0863 -10.1965 -3.0089 REMARK 3 T TENSOR REMARK 3 T11: 0.2275 T22: 0.2126 REMARK 3 T33: 0.1389 T12: 0.0488 REMARK 3 T13: -0.0008 T23: 0.0166 REMARK 3 L TENSOR REMARK 3 L11: 0.1110 L22: 0.1301 REMARK 3 L33: 0.2933 L12: 0.0838 REMARK 3 L13: 0.0296 L23: 0.0286 REMARK 3 S TENSOR REMARK 3 S11: -0.1858 S12: -0.2234 S13: -0.1758 REMARK 3 S21: 0.2987 S22: 0.2204 S23: 0.1181 REMARK 3 S31: 0.1452 S32: 0.0538 S33: 0.0063 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 231:254) REMARK 3 ORIGIN FOR THE GROUP (A): -3.3553 -4.5216 -22.0585 REMARK 3 T TENSOR REMARK 3 T11: 0.1823 T22: 0.1618 REMARK 3 T33: 0.1504 T12: 0.0335 REMARK 3 T13: -0.0357 T23: -0.0223 REMARK 3 L TENSOR REMARK 3 L11: 0.3958 L22: 0.3048 REMARK 3 L33: 0.1170 L12: -0.2908 REMARK 3 L13: -0.2333 L23: 0.0739 REMARK 3 S TENSOR REMARK 3 S11: 0.0660 S12: 0.1381 S13: -0.0290 REMARK 3 S21: -0.2076 S22: -0.1255 S23: 0.1332 REMARK 3 S31: -0.1375 S32: -0.1586 S33: 0.0219 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN A AND RESID 255:277) REMARK 3 ORIGIN FOR THE GROUP (A): -4.8244 -7.6590 -14.0257 REMARK 3 T TENSOR REMARK 3 T11: 0.1100 T22: 0.1319 REMARK 3 T33: 0.1585 T12: -0.0059 REMARK 3 T13: 0.0089 T23: -0.0201 REMARK 3 L TENSOR REMARK 3 L11: 0.2149 L22: 0.4361 REMARK 3 L33: 0.3766 L12: -0.3309 REMARK 3 L13: -0.0800 L23: 0.2179 REMARK 3 S TENSOR REMARK 3 S11: 0.0009 S12: 0.1814 S13: -0.0070 REMARK 3 S21: 0.0144 S22: -0.0407 S23: 0.1255 REMARK 3 S31: -0.0151 S32: -0.1859 S33: -0.0091 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN A AND RESID 278:305) REMARK 3 ORIGIN FOR THE GROUP (A): 19.4117 -4.3089 -12.8504 REMARK 3 T TENSOR REMARK 3 T11: 0.1499 T22: 0.1737 REMARK 3 T33: 0.2297 T12: -0.0148 REMARK 3 T13: -0.0157 T23: -0.0462 REMARK 3 L TENSOR REMARK 3 L11: 0.2561 L22: 0.4246 REMARK 3 L33: 0.1791 L12: 0.0323 REMARK 3 L13: 0.2098 L23: 0.2419 REMARK 3 S TENSOR REMARK 3 S11: -0.1219 S12: -0.0908 S13: 0.4132 REMARK 3 S21: 0.1030 S22: 0.1635 S23: -0.2914 REMARK 3 S31: -0.0897 S32: 0.1841 S33: -0.0190 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN A AND RESID 306:312) REMARK 3 ORIGIN FOR THE GROUP (A): 8.4244 -7.4726 -16.5024 REMARK 3 T TENSOR REMARK 3 T11: 0.1170 T22: 0.1020 REMARK 3 T33: 0.1350 T12: -0.0000 REMARK 3 T13: 0.0062 T23: -0.0036 REMARK 3 L TENSOR REMARK 3 L11: 0.0318 L22: 0.0579 REMARK 3 L33: 0.0736 L12: -0.0395 REMARK 3 L13: -0.0185 L23: 0.0577 REMARK 3 S TENSOR REMARK 3 S11: -0.0322 S12: -0.0367 S13: -0.0402 REMARK 3 S21: -0.0128 S22: 0.0676 S23: -0.1069 REMARK 3 S31: 0.0021 S32: -0.0442 S33: 0.0009 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: (CHAIN A AND RESID 313:325) REMARK 3 ORIGIN FOR THE GROUP (A): 6.3884 -13.3273 -25.6070 REMARK 3 T TENSOR REMARK 3 T11: 0.1148 T22: 0.1075 REMARK 3 T33: 0.1189 T12: -0.0074 REMARK 3 T13: 0.0108 T23: 0.0085 REMARK 3 L TENSOR REMARK 3 L11: 0.1234 L22: 0.1711 REMARK 3 L33: 0.2924 L12: -0.0076 REMARK 3 L13: 0.1513 L23: 0.1556 REMARK 3 S TENSOR REMARK 3 S11: 0.0439 S12: 0.0988 S13: 0.0880 REMARK 3 S21: -0.0149 S22: -0.0078 S23: 0.0599 REMARK 3 S31: -0.0592 S32: -0.0615 S33: -0.0016 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: (CHAIN A AND RESID 326:341) REMARK 3 ORIGIN FOR THE GROUP (A): 9.6890 -19.0746 -19.9825 REMARK 3 T TENSOR REMARK 3 T11: 0.1218 T22: 0.1058 REMARK 3 T33: 0.1087 T12: -0.0018 REMARK 3 T13: 0.0026 T23: 0.0022 REMARK 3 L TENSOR REMARK 3 L11: 0.2531 L22: 0.2253 REMARK 3 L33: 0.1264 L12: -0.1608 REMARK 3 L13: 0.0285 L23: 0.0777 REMARK 3 S TENSOR REMARK 3 S11: -0.0021 S12: -0.0096 S13: -0.0299 REMARK 3 S21: 0.0674 S22: 0.0433 S23: -0.0389 REMARK 3 S31: 0.0645 S32: 0.0257 S33: 0.0052 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: (CHAIN A AND RESID 342:365) REMARK 3 ORIGIN FOR THE GROUP (A): 8.1790 -14.9520 -37.6158 REMARK 3 T TENSOR REMARK 3 T11: 0.1708 T22: 0.1501 REMARK 3 T33: 0.1206 T12: -0.0100 REMARK 3 T13: -0.0013 T23: 0.0287 REMARK 3 L TENSOR REMARK 3 L11: 0.3923 L22: 0.2311 REMARK 3 L33: 0.6836 L12: 0.0147 REMARK 3 L13: 0.4417 L23: 0.2975 REMARK 3 S TENSOR REMARK 3 S11: -0.0327 S12: 0.2025 S13: 0.1797 REMARK 3 S21: -0.1485 S22: -0.0061 S23: 0.0013 REMARK 3 S31: -0.1502 S32: 0.0620 S33: -0.0008 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: (CHAIN A AND RESID 366:381) REMARK 3 ORIGIN FOR THE GROUP (A): 2.2388 -24.6246 -38.9760 REMARK 3 T TENSOR REMARK 3 T11: 0.1616 T22: 0.1621 REMARK 3 T33: 0.1225 T12: 0.0140 REMARK 3 T13: -0.0369 T23: -0.0065 REMARK 3 L TENSOR REMARK 3 L11: 0.1358 L22: 0.2435 REMARK 3 L33: 0.1149 L12: 0.0486 REMARK 3 L13: 0.0998 L23: -0.1102 REMARK 3 S TENSOR REMARK 3 S11: 0.2023 S12: 0.1149 S13: -0.1316 REMARK 3 S21: -0.0467 S22: -0.0416 S23: 0.0884 REMARK 3 S31: 0.2781 S32: -0.0567 S33: 0.0025 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: (CHAIN A AND RESID 382:399) REMARK 3 ORIGIN FOR THE GROUP (A): 14.5351 -19.1540 -22.7644 REMARK 3 T TENSOR REMARK 3 T11: 0.1178 T22: 0.1082 REMARK 3 T33: 0.1144 T12: 0.0091 REMARK 3 T13: -0.0014 T23: 0.0024 REMARK 3 L TENSOR REMARK 3 L11: 0.3326 L22: 0.2008 REMARK 3 L33: 0.3242 L12: 0.0133 REMARK 3 L13: 0.1774 L23: 0.2542 REMARK 3 S TENSOR REMARK 3 S11: 0.0031 S12: 0.0165 S13: -0.0497 REMARK 3 S21: 0.0346 S22: 0.0521 S23: -0.0653 REMARK 3 S31: 0.1006 S32: 0.0921 S33: 0.0256 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: (CHAIN A AND RESID 400:416) REMARK 3 ORIGIN FOR THE GROUP (A): 10.2561 -13.4993 -19.2894 REMARK 3 T TENSOR REMARK 3 T11: 0.1119 T22: 0.1027 REMARK 3 T33: 0.1057 T12: -0.0055 REMARK 3 T13: 0.0045 T23: 0.0013 REMARK 3 L TENSOR REMARK 3 L11: 0.2752 L22: 0.5443 REMARK 3 L33: 0.5098 L12: -0.3259 REMARK 3 L13: 0.1064 L23: 0.3202 REMARK 3 S TENSOR REMARK 3 S11: -0.0138 S12: 0.0095 S13: 0.0532 REMARK 3 S21: 0.0552 S22: 0.0464 S23: -0.0097 REMARK 3 S31: 0.0284 S32: 0.0310 S33: -0.0019 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 6F4Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 30-NOV-17. REMARK 100 THE DEPOSITION ID IS D_1200007740. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-MAY-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 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 : 95694 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.120 REMARK 200 RESOLUTION RANGE LOW (A) : 49.910 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 11.10 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 32.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.12 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.16 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.3 REMARK 200 DATA REDUNDANCY IN SHELL : 9.90 REMARK 200 R MERGE FOR SHELL (I) : 1.10000 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: PHASER REMARK 200 STARTING MODEL: 6F4P REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BIS-TRIS PH 6.0, 19.3 % PEG3350, REMARK 280 0.002 M MNCL2, 300 NL SITTING DROPS (SAMPLE:WELL, 1:1 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 24.70300 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 38.88450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.53650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.88450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.70300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.53650 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 VAL B 129 REMARK 465 PRO B 130 REMARK 465 ARG B 131 REMARK 465 ARG B 132 REMARK 465 LEU B 133 REMARK 465 GLY B 134 REMARK 465 PRO B 135 REMARK 465 LYS B 136 REMARK 465 SER B 139 REMARK 465 ARG B 140 REMARK 465 ILE B 141 REMARK 465 ARG B 142 REMARK 465 LYS B 143 REMARK 465 LEU B 144 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 GLN A 219 CD OE1 NE2 REMARK 470 GLU A 247 CG CD OE1 OE2 REMARK 470 GLN A 344 CD OE1 NE2 REMARK 470 ASP A 353 CG OD1 OD2 REMARK 470 LEU A 356 CG CD1 CD2 REMARK 470 LYS A 378 CG CD CE NZ 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 H31 TRS A 503 O HOH A 636 1.44 REMARK 500 HD1 HIS A 214 O HOH A 606 1.48 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 ARG A 189 60.04 38.32 REMARK 500 PHE A 199 -55.80 -129.89 REMARK 500 PHE A 199 -55.80 -131.56 REMARK 500 ILE A 263 -59.88 -120.52 REMARK 500 CYS A 275 61.82 37.63 REMARK 500 ASN A 367 66.25 -151.84 REMARK 500 LYS A 397 -1.72 72.27 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 960 DISTANCE = 6.08 ANGSTROMS 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 106.9 REMARK 620 3 HIS A 400 NE2 84.6 85.2 REMARK 620 4 OGA A 502 O2' 86.0 166.4 92.0 REMARK 620 5 OGA A 502 O1 161.6 91.3 99.8 76.1 REMARK 620 6 HOH A 786 O 86.3 87.4 166.0 97.9 92.2 REMARK 620 N 1 2 3 4 5 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 OGA 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 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 505 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: 6F4O RELATED DB: PDB REMARK 900 RELATED ID: 6F4P 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 6F4Q A 183 416 UNP Q8N371 KDM8_HUMAN 221 454 DBREF 6F4Q B 129 144 UNP P62753 RS6_HUMAN 129 144 SEQADV 6F4Q HIS A 162 UNP Q8N371 EXPRESSION TAG SEQADV 6F4Q HIS A 163 UNP Q8N371 EXPRESSION TAG SEQADV 6F4Q HIS A 164 UNP Q8N371 EXPRESSION TAG SEQADV 6F4Q HIS A 165 UNP Q8N371 EXPRESSION TAG SEQADV 6F4Q HIS A 166 UNP Q8N371 EXPRESSION TAG SEQADV 6F4Q HIS A 167 UNP Q8N371 EXPRESSION TAG SEQADV 6F4Q SER A 168 UNP Q8N371 EXPRESSION TAG SEQADV 6F4Q SER A 169 UNP Q8N371 EXPRESSION TAG SEQADV 6F4Q GLY A 170 UNP Q8N371 EXPRESSION TAG SEQADV 6F4Q VAL A 171 UNP Q8N371 EXPRESSION TAG SEQADV 6F4Q ASP A 172 UNP Q8N371 EXPRESSION TAG SEQADV 6F4Q LEU A 173 UNP Q8N371 EXPRESSION TAG SEQADV 6F4Q GLY A 174 UNP Q8N371 EXPRESSION TAG SEQADV 6F4Q THR A 175 UNP Q8N371 EXPRESSION TAG SEQADV 6F4Q GLU A 176 UNP Q8N371 EXPRESSION TAG SEQADV 6F4Q ASN A 177 UNP Q8N371 EXPRESSION TAG SEQADV 6F4Q LEU A 178 UNP Q8N371 EXPRESSION TAG SEQADV 6F4Q TYR A 179 UNP Q8N371 EXPRESSION TAG SEQADV 6F4Q PHE A 180 UNP Q8N371 EXPRESSION TAG SEQADV 6F4Q GLN A 181 UNP Q8N371 EXPRESSION TAG SEQADV 6F4Q SER A 182 UNP Q8N371 EXPRESSION TAG SEQADV 6F4Q ALA A 217 UNP Q8N371 CYS 255 ENGINEERED MUTATION SEQADV 6F4Q ALA A 232 UNP Q8N371 CYS 270 ENGINEERED MUTATION SEQADV 6F4Q CYS A 275 UNP Q8N371 GLN 313 ENGINEERED MUTATION SEQADV 6F4Q ALA A 295 UNP Q8N371 CYS 333 ENGINEERED MUTATION SEQADV 6F4Q ALA A 384 UNP Q8N371 CYS 422 ENGINEERED MUTATION SEQADV 6F4Q CYS B 138 UNP P62753 ALA 138 ENGINEERED MUTATION 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 ALA MET GLN LYS TRP SER LEU GLU TYR ILE SEQRES 6 A 255 GLN GLU ILE ALA GLY ALA 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 CYS 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 ALA 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 ALA 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 SEQRES 1 B 16 VAL PRO ARG ARG LEU GLY PRO LYS ARG CYS SER ARG ILE SEQRES 2 B 16 ARG LYS LEU HET MN A 501 1 HET OGA A 502 13 HET TRS A 503 20 HET GOL A 504 14 HET GOL A 505 14 HETNAM MN MANGANESE (II) ION HETNAM OGA N-OXALYLGLYCINE HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETNAM GOL GLYCEROL HETSYN TRS TRIS BUFFER HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 MN MN 2+ FORMUL 4 OGA C4 H5 N O5 FORMUL 5 TRS C4 H12 N O3 1+ FORMUL 6 GOL 2(C3 H8 O3) FORMUL 8 HOH *361(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 TYR A 350 5 9 HELIX 10 AB1 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 SSBOND 1 CYS A 275 CYS B 138 1555 1555 2.05 LINK NE2 HIS A 321 MN MN A 501 1555 1555 2.22 LINK OD2 ASP A 323 MN MN A 501 1555 1555 2.14 LINK NE2 HIS A 400 MN MN A 501 1555 1555 2.27 LINK MN MN A 501 O2' OGA A 502 1555 1555 2.17 LINK MN MN A 501 O1 OGA A 502 1555 1555 2.19 LINK MN MN A 501 O HOH A 786 1555 1555 2.22 SITE 1 AC1 5 HIS A 321 ASP A 323 HIS A 400 OGA A 502 SITE 2 AC1 5 HOH A 786 SITE 1 AC2 14 TYR A 272 TRP A 310 SER A 318 HIS A 321 SITE 2 AC2 14 ASP A 323 ASN A 327 LEU A 329 LYS A 336 SITE 3 AC2 14 HIS A 400 VAL A 402 SER A 412 TRP A 414 SITE 4 AC2 14 MN A 501 HOH A 764 SITE 1 AC3 14 LEU A 200 VAL A 201 GLY A 203 GLN A 326 SITE 2 AC3 14 TYR A 350 LYS A 372 PHE A 373 VAL A 396 SITE 3 AC3 14 HOH A 627 HOH A 636 HOH A 648 HOH A 685 SITE 4 AC3 14 HOH A 696 HOH A 865 SITE 1 AC4 6 ARG A 196 ARG A 268 ASP A 269 SER A 296 SITE 2 AC4 6 LEU A 297 HOH A 630 SITE 1 AC5 7 ARG A 189 PRO A 190 GLU A 266 ASP A 293 SITE 2 AC5 7 TYR A 294 HOH A 693 HOH A 720 CRYST1 49.406 65.073 77.769 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 0.020240 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015367 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012859 0.00000